Novel receptor-type phosphotyrosine phosphatase-alpha

ABSTRACT

A novel receptor-type protein tyrosine phosphatase (RPTP) protein or glycoprotein and the DNA coding therefor is expressed in a wide variety of mammalian tissues. Included in this family of proteins are human RPTPα, human RPTPβ and human RPTPγ. The RPTP protein or glycoprotein may be produced by recombinant means. Antibodies to the proteins, methods for measuring the quantity of the proteins, methods for screening compounds, such as drugs, which can bind to the proteins and inhibit or stimulate their activity, are provided.

The present application is a continuation-in-part of U.S. applicationSer. No. 07/654,188, filed Feb. 26, 1991, which was acontinuation-in-part of U.S. application Ser. No. 07/551,270, filed Jul.11, 1990, now abandoned. The entire contents of both of the aboveapplications are hereby incorporated by reference.

1. INTRODUCTION

The invention in the field of biochemistry and cell and molecularbiology relates to novel receptor-type protein tyrosine phosphataseproteins or glycoproteins, termed RPTPα, RPTPβ and RPTPγ (alsodesignated R-PTPase-α, β and γ), DNA coding therefor, methods forproduction and identification of the proteins, and methods for screeningcompounds capable of binding to and inhibiting or stimulating PTPaseenzymatic activity.

2. BACKGROUND OF THE INVENTION

The identification of several growth factor receptors and retroviraloncogenes as tyrosine-specific protein kinases indicated that proteinphosphorylation on tyrosine residues plays a key role in cellular growthcontrol. This notion has recently received support by the observationthat the level of tyrosine phosphorylation of enzymes thought to play animportant role in signal transduction (such as phospholipase C)correlates with their increased activity upon growth factor stimulation,thus establishing a functional role for tyrosine phosphorylation(Ullrich, A., et al., Cell 61:203-212 (1990)).

The degree and pattern of phosphorylation of tyrosine residues oncellular proteins are regulated by the opposing activities ofprotein-tyrosine kinases (PTKases; ATP:protein-tyrosineO-phosphotransferase, EC 2.7.1.112) and protein-tyrosine-phosphatases(PTPases; protein-tyrosine-phosphate phosphohydrolase, EC 3.1.3.48). Thestructural characteristics and evolution of PTKases as well as theirrole in the regulation of cell growth have been reviewed (Hunter, T., etal., Annu. Rev. Biochem. 54:897-930 (1985); Ullrich, A., et al., supra).

2.1. PTKases

Tyrosine kinases comprise a discrete family of enzymes having commonancestry with, but major differences from, serine/threonine-specificprotein kinases (Hanks, S. K. et al., (1988) Science 241, 42-52). Themechanisms leading to changes in activity of tyrosine kinases are bestunderstood for receptor-type tyrosine kinases which have a transmembranetopology (Ullrich, A., et al., supra). With such kinases, the binding ofspecific ligands to the extracellular domain of these enzymes is thoughtto induce their oligomerization leading to an increase in tyrosinekinase activity and activation of the signal transduction pathways(Ullrich, A. et al., supra). The importance of this activity issupported by the knowledge that dysregulation of kinase activity throughmutation or over-expression is a mechanism for oncogenic transformation(Hunter, T et al., supra; Ullrich, A. et al., 1990, supra).

2.2. PTPases

The protein phosphatases are composed of at least two separate anddistinct families (Hunter, T. Cell, 58:1013-1016 (1989)), the proteinserine/threonine phosphatases and the protein tyrosine phosphatases.This is in contrast to protein kinases, which show clear sequencesimilarity between serine/threonine-specific and tyrosine-specificenzymes.

There appear to be two varieties of PTPase molecules. The first group iscomprised of small, soluble enzymes that contain a single conservedphosphatase catalytic domain, and include (1) placental PTPase 1B(Charbonneau, H. et al., Proc. Natl. Acad. Sci. 86:5252-5256 (1989);Chernoff, J. et al., Proc. Natl. Acad. Sci. USA 87:2735-2789 (1990)),(2) T-cell PTPase (Cool, D. E. et al., Proc. Natl. Acad. Sci. USA86:5257-5261 (1989)), and (3) rat brain PTPase (Guan, K., et al., Proc.Natl. Acad. Sci. USA, 87:1501-1505 (1990).

The second group is made up of the more complex, receptor-linkedPTPases, termed R-PTPases (or RPTPs), which are of high molecular weightand contain two tandemly repeated conserved domains separated by 56-57amino acids. One example of RPTPs are the leukocyte common antigens(LCA) (Ralph, S. J., EMBO J., 6:1251-1257 (1987); Charbonneau, H., etal., Proc. Natl. Acad. Sci. USA, 85:7182-7186 (1988)). LCA, also knownas CD45, T200 and Ly-5 (reviewed in Thomas, M. L., Ann. Rev. Immunol.7:339-369 (1989)) comprises a group of membrane glycoproteins expressedexclusively in hemopoietic (except late erythroid) cells, derived from acommon gene by alternative splicing events involving the amino terminusof the proteins. Whereas the precise function of CD45 is unknown, manystudies have implicated these antigens in a number of processes,including the activity of cytotoxic T lymphocytes and natural killercells, IL-2 receptor expression, B-cell differentiation, and Tlymphocyte proliferation (Pingel, J. T. et al., Cell 58:1055-1065(1989)).

Other examples of RPTPs are the LCA-related protein, LAR (Streuli, M.,et al., J. Exp. Med., 168:1523-1530 (1988)), and the LAR-relatedDrosophila proteins DLAR and DPTP (Streuli, M., et al., Proc. Natl.Acad. Sci. USA, 86:8698-8702 (1989)). Jirik et al. screened a cDNAlibrary derived from the human hepatoblastoma cell line, HepG2, with aprobe encoding the two PTPase domains of LCA (FASEB J. 4:A2082 (1990),abstr. 2253) and discovered a cDNA clone encoding a new RPTP, namedHe-PTP. The HePTP gene appeared to be expressed in a variety of humanand murine cell lines and tissues.

While we are beginning to understand more about the structure anddiversity of the PTPases, much remains to be learned about theircellular functions. It has been suggested (Tonks, N. K., et al.,Biochemistry, 27:8695-8701 (1988)) that the small, soluble PTPaseenzymes may have a “housekeeping” function. On the other hand, the RPTPswould be expected to be more restricted in their activities because oftheir location in the cell membrane and their potential regulation byextracellular ligands. Regarding the role of LCA (CD45) in T cells, itwas found that T cell clones deficient in the expression of LCA failedto proliferate when stimulated by a specific antigen or by cross-linkingof CD3 (Pingel, J. T., et al., supra). PTPase cross-linking inhibits Tcell receptor CD3-mediated activation in human T cells (Kiener, P. A. etal., J. Immunol. 143:23-28 (1989)). The PTPase activity of LCA plays arole in the activation of pp56^(lck), a lymphocyte-specific PTKase(Mustelin, T., et al., Proc. Natl. Acad. Sci. USA, 86:6302-6306 (1989);Ostergaard, H. L., et al., Proc. Natl. Acad. Sci. USA, 86:8959-8963(1989)). These authors hypothesized that the phosphatase activity of LCAactivates pp56^(lck) by dephosphorylation of a C-terminal tyrosineresidue, which may, in turn, be related to T-cell activation.

Using site-directed mutagenesis to determine which of four conservedcysteines in LCA (two per phosphatase domain) was required for enzymeactivity toward artificial substrates, Streuli et al. (1989, supra)found that only one cysteine residue (residue 177 of LCA phosphatasedomain-1) of LCA was essential for activity, indicating that, mostlikely, only the first phosphatase domain has enzymatic activity.However, the possibility that the second domain can dephosphorylate adifferent substrate was not excluded. More recently, Streuli et. al.(EMBO J., 9:2399-2407 (1990)) determined that the second conserveddomain of LCA (and of LAR) lacked detectable phosphatase activity butsequences within the domain could influence substrate specificity.

In order to better understand and to be able to control phosphotyrosinemetabolism, one must comprehend not only the role of kinase activity,but also the action of phosphatase enzymes as well. Elevation ofcellular phosphotyrosine may occur through mechanisms not involving theactivation of a tyrosine kinase itself. For instance, expression of thev-crk oncogene, though not a tyrosine kinase itself, induces thephosphorylation of tyrosine residues through a poorly understoodmechanism (Mayer, B. J. et al. (1988) Nature 332, 272-275). Potentially,such an outcome could result from either mutation of the substrate orthrough a general decrease in cellular phosphatase activity, especiallyin view of the normally high turnover rate of cellulartyrosine-phosphate (Sefton, B. M. et al. (1980) Cell 20, 807-816). Thelatter possibility is suggested by the demonstration that tyrosinephosphatase inhibitors can “reversibly transform” cells (Klarlund, J. K.Cell 41:707-717 (1985)). PTPases could therefore be viewed as potentialrecessive oncogenes.

It is becoming clear that dephosphorylation of tyrosine can by itselffunction as an important regulatory mechanism. Dephosphorylation of aC-terminal tyrosine residue stimulates tyrosine kinase activity in thesrc-family of tyrosine kinases (Hunter, T. (1987) Cell 49, 1-4).Tyrosine dephosphorylation has been suggested to be an obligatory stepin the mitotic activation of the MPF (maturation promoting factor)kinase (Morla, A. O. et. al. (1989) Cell 58, 193-203). Lastly, mutantanalysis of primitive eukaryotes has established crucial roles forserine phosphatase in cellular physiology (Cyert, M. S. et al. (1989)Cell 57, 891-893). These observations point out the need in the art forincreasing our understanding of the mechanisms that regulate tyrosinephosphatase activity.

It is clear in the art that further analysis of structure-functionrelationships among these membrane receptors are needed to gainimportant understanding of the mechanisms of cell growth,differentiation, and oncogenesis.

3. SUMMARY OF THE INVENTION

The inventors have conceived of a role for RPTPs in cellular controlmechanisms, both as potential anti-oncogenes, and as effectors in anewly discovered mechanism of transmembrane signalling. They thereforeundertook a search for an RPTP potentially involved in such processes,and describe herein the identification of a novel, widely expressedmember of the RPTP family, which has a transmembrane topology.Importantly, its extracellular domain is unrelated to any other RPTPheretofore described. The novel RPTPs, in a manner analogous to receptortyrosine kinases, are subject to direct regulation by a variety ofdifferent extracellular ligands.

The present invention thus provides a human receptor-type proteintyrosine phosphatase (RPTP) protein or glycoprotein molecule other thanleucocyte common antigen (LCA or CD45) and leucocyte commonantigen-related protein (LAR), a functional derivative of the human RPTPor a homolog of the human RPTP in another mammalian species. When themolecule is of natural origin, it is substantially free of otherproteins or glycoproteins with which it is natively associated. Thisnaturally-occurring molecule is normally present in mammalian liver,kidney and brain. Alternatively, the RPTP molecule may not be of naturalorigin, such as one prepared by chemical or recombinant means.

The substantially pure RPTP protein or glycoprotein of the invention maybe produced by biochemical purification of the glycoprotein of naturalorigin; alternatively, the RPTP may be produced by recombinant means inprokaryotic or eukaryotic hosts.

In particular, the invention is directed to the molecule RPTPα,preferably human RPTPα having the amino acid sequence (SEQ ID NO:1)shown in FIGS. 4 and 8, or a functional derivative thereof. In anotherembodiment, the invention is directed to human RPTPβ. In yet anotherembodiment, the invention is directed to human RPTPγ.

The invention is further directed to a nucleic acid molecule consistingessentially of a nucleotide sequence encoding RPTPα of mouse or humanorigin, or RPTPβ or RPTPγ, both of human origin, or a functionalderivative thereof. The nucleic acid molecule may be in the form of cDNAor genomic DNA. Preferably, the is nucleic acid molecule has thenucleotide sequence of human RPTPα-encoding DNA, SEQ ID NO:2, also shownin FIG. 8. The invention is further directed to the nucleic acidmolecule in the form of an expression vehicle, as well as prokaryoticand eukaryotic hosts transformed with the nucleic acid molecule.

Also included in the present invention is a process for preparing anRPTP protein or glycoprotein of this invention, or a functionalderivative thereof, comprising:

-   -   (a) culturing a host capable of expressing the protein,        glycoprotein or functioanl derivative under culturing        conditions;    -   (b) expressing the protein, glycprotein or functional        derivative; and    -   (c) recovering the protein, glycoprotein or functional        derivative from the culture.

The invention is directed to an antibody, polyclonal, monoclonal, orchimeric, specific for the RPTPα protein or glycoprotein.

The invention is also directed to a method for detecting the presence ofnucleic acid encoding a normal or mutant RPTP in a subject comprising:

-   -   (a) contacting a cell or an extract thereof from the subject        with an oligonucleotide probe encoding at least a portion of the        normal or mutant RPTP under hybridizing conditions; and    -   (b) measuring the hybridization of the probe to the nucleic acid        of the cell, thereby detecting the presence of the nucleic acid.        The DNA can be selectively amplified, using the polymerase chain        reaction, prior to assay.

The invention is further directed to a method for detecting thepresence, or measuring the quantity of an RPTP in cell or in a subjectcomprising:

-   -   (a) contacting said cell or an extract thereof with an antibody        specific for an epitope of the RPTP; and    -   (b) detecting the binding of the antibody to the cell or extract        thereof, or measuring the quantity of antibody bound,        thereby detecting the presence or measuring the quantity of the        RPTP.

The present invention is also directed to methods for identifying andisolating a compound capable of binding to an RPTP from a chemical orbiological preparation comprising:

-   -   (a) attaching the RPTP or the ligand-binding portion thereof to        a solid phase matrix;    -   (b) contacting the chemical or biological preparation with the        solid phase matrix allowing the compound to bind, and washing        away any unbound material;    -   (c) detecting the presence of the compound bound to the solid        phase; and, for purposes of isolation,    -   (d) eluting the bound compound, thereby isolating the compound.

Finally, the invention includes a method for identifying a compoundcapable of stimulating or inhibiting the enzymatic activity of a RPTP,comprising:

-   -   (a) contacting the compound with the RPTP in pure form, in a        membrane preparation, or in a whole live or fixed cell;    -   (b) incubating the mixture in step (a) for a sufficient        interval;    -   (c) measuring the enzymatic activity of the RPTP;    -   (d) comparing the enzymatic activity to that of the RPTP        incubated without the compound,        thereby determining whether the compound stimulates or inhibits        the activity.

In all the above methods, the RPTP is preferably RPTPα, most preferably,human RPTPα.

4. DESCRIPTION OF THE FIGURES

FIG. 1 shows the nucleotide sequence (SEQ ID NO:4) and predicted aminoacid sequence (SEQ ID NO:3) of murine RPTPα.

FIG. 1A (1A(1)-1A((3)) shows the sequence of the phage λ-109 cDNA insert(numbering refers to nucleotide positions) and predicted RPTPα proteinsequence (using the standard one-letter amino acid code). The putativetrans-membrane domain (amino acids 143 to 166) is underlined as well asthe potential N-linked glycosylation sites in the extracellular domain.The borders of homology between the tandemly repeated PTPase domains (Iand II) are indicated by square brackets. Cysteine (C) residuesconserved in the catalytic domain of all known RPTPs are alsounderlined.

FIG. 1B shows a schematic structure of a λ-109 cDNA clone containing theRPTPα coding sequence. RPTP domains I and II are indicated as blackboxes, the transmembrane domain is shaded. The start of the N-terminallytruncated PTP-ΔC protein (see FIG. 3, below) is indicated by an arrow(at amino acid 214). The positions of restriction sites used forgenerating nested deletions for sequencing are indicated. Abbreviations:TM, transmembrane domain; B, BamHI site; Bs, BstEII site; N, NcoI site;Nd, NdeI site; P, PstI site; R, EcoRI site; S: SacII site; St, StuIsite.

FIG. 2 is a Northern blot showing expression of the murine RPTPα mRNA. 5μg of Poly A⁺ RNA from mouse tissues and cell lines was fractionated onformaldehyde-containing agarose gels and subjected to Northern analysisusing as a probe the entire RPTPα cDNA. The positions of the 28S and 18Sribosomal RNA, are indicated. Lanes: 1, kidney; 2, lung; 3, heart; 4,stomach; 5, brain; 6, spleen; 7, liver; 8, NIH-3T3 fibroblast cell line(Honegger, A. M. et al. (1987) Cell 51, 199-209); 9, BAF prepro-Blymphoid cell line (Palacios, R. et al. (1985) Cell 41, 727-734).

FIG. 3 is a gel pattern showing results of PAGE of immunoprecipitates ofthe murine RPTPα protein. COS cells were transiently transfected usingthe DEAE-dextran method with a negative control plasmid (expressionvector, pLSV without insert), with either pLSV-PTP-α (the sameexpression vector containing the RPTPα cDNA), or with the expressionvector PLSVΔC, designed to express a truncated RPTPα protein (PTP-ΔC,amino-acids 214-794, from which the transmembrane and extracellulardomains have been removed). After metabolic labelling with[³⁵S]-methionine, immunoprecipitation was performed using eitherpre-immune serum (lanes 1 and 2) or with an antiserum designated “2A”(lanes 3-8), raised against a synthetic peptide corresponding to theC-terminus of the RPTPα protein in the absence or presence of 100 μg ofthe immunizing peptide. Sizes of molecular weight markers are shown inkDa at the left margin. The arrow marks the position of the 130 kDaRPTPα protein (lane 5). Lane 1: pLSV, pre-immune serum; lane 2:pLSV-PTP-α, pre-immune serum; lane 3: pLSV, antiserum 2A; lane 4: pLSV,antiserum 2A in the presence of synthetic peptide; lane 5: pLSV-PTP-α,antiserum 2A; lane 6: pLSV-PTP-α, antiserum 2A in the presence ofsynthetic peptide; lane 7: PLSVΔC, antiserum 2A; lane 8: pLSVΔC,antiserum 2A in the presence of synthetic peptide.

FIG. 4 shows the structure of human RPTPα deduced from the sequence ofcDNA clones.

FIG. 4A is a composite restriction map [3615 base pairs (bp)] ofoverlapping clones 31-4 and 27-1, which together contain the entirecoding region of human RPTPα.

FIG. 4B shows the relative positions of clones 31-4 and 27-1. Bothstrands of each clone were sequenced in their entirety by using a seriesof oligonucleotide primers. The hatched region in clone 31-4 correspondsto the fragment used as probe for the Northern blot (see FIG. 6, below)as well as for the chromosome assignment.

FIG. 4C shows the different domains of RPTPα.

FIG. 4D provides a comparison of the amino acid sequences of human(line 1) [SEQ ID NO:1] and mouse (line 2) [SEQ ID NO:3] RPTPα. Thesingle-letter amino acid code is used. Only the differences are shown.The dashed line indicates a stretch of amino acids not present in themouse sequence. The coding portion of human RPTPα, and its positionrelative to clones 31-4 and 27-1 (FIG. 4B), is shown at the top. Thefollowing regions are designated in encircled Roman numerals: signalpeptide (I), extracellular domain with potential N-glycosylation sitesfor the human protein underlined (II), transmembrane (III),juxtamembrane (IV), first phosphatase domain (V), interdomain (VI),second phosphatase domain (VII), C terminus (VIII).

FIG. 5 shows a comparison of the amino acid sequences of the first (FIG.5A) and second (FIG. 5B) conserved phosphatase domains of human RPTPsLCA, a, β and γ. CON is the consensus sequence: a capital letterindicates complete agreement, while a small letter indicates agreementamong two or three of the four sequences. A dash indicates lack ofconsensus.

FIG. 6 shows a Northern blot pattern indicating relative expression ofhuman RPTPα in various tissues and cell lines, as determined byhybridization with RPTPα probe (Upper) and β-actin probe (Lower). TotalRNA (five left lanes) or poly (A)⁺ RNA (five right lanes) samples fromthe indicated human cell lines or tissues were analyzed. A431 is a humanepidermoid carcinoma cell line; HEL is an erythroleukemia cell line; allother lanes represent flash-frozen tissues samples (HUVEC—humanumbilical vein endothelial cells).

FIG. 7 is a matrix diagram which shows the chromosomal localization ofhuman RPTPα based on analysis of a panel of 17 rodent-human somatic cellhybrids. A completely stippled box indicates that the hybrid containedthe human chromosome indicated in the upper row; lower-right stipplingindicates presence of the long arm of (or part of the long arm,indicated by a smaller fraction of stippling) of the chromosome;upper-left stippling indicates presence of the short arm (or partialshort arm) of the chromosome; an open box indicates absence of thechromosome. The boxes in the column for chromosome 20 are blackened tohighlight correlation of presence of this chromosome (or chromosomeregion) with the presence of the RPTPα gene. The pattern of retention ofthe human RPTPα sequences in the hybrids is shown at right (RPTPα):presence of the gene is indicated by a “+” in a black box; absence ofthe gene is indicated by a “−” in an open box.

FIG. 8 shows the complete nucleotide sequence (SEQ ID NO:2) and deducedamino acid sequence (SEQ ID NO:1) of human RPTPα.

5. DETAILED DESCRIPTION OF THE INVENTION

Through the use of recombinant DNA methods, the present inventors haveidentified novel mammalian receptor-type (transmembrane) proteintyrosine phosphatases (PTPase; EC 3.1.3.48). The murine RPTPα has 794amino acids, whereas the human RPTPα has 802 amino acids. In view of itsreceptor-like structure, and the likelihood that it is part of a family,the inventors have termed this protein, RPTPα (receptor protein tyrosinephosphatase alpha). The family is designated herein as “RPTP.”

RPTPα has an intracellular domain homologous to the catalytic domains ofother tyrosine phosphatases. The inventors have further characterizedthe 142 amino acid extracellular domain (including signal peptide) ashaving a high serine and threonine content (32%) and 8 potentialN-glycosylation sites. The inventors have produced cDNA clones codingfor the novel protein, and expressed the protein from eukaryotic hosts.Northern analysis has been used to identify the natural expression ofthe protein in various cells and tissues. They have further produced apolyclonal antibody to the protein by immunization with a syntheticpeptide of RPTPα, which identifies a 130 kDa protein in cellstransfected with a cDNA clone encoding a portion of RPTPα.

Remarkably, in addition to being composed of intracellular domainshaving enzymatic activity, the receptor family to which RPTPs belongincludes transmembrane proteins having and N-terminal extracellulardomains; this is analogous to the tyrosine kinase enzyme family (Tonks,N. K. et al. (1988) Biochemistry 27, 8695-8701; Charbonneau, H. et al.(1988) Proc. Natl. Acad. Sci. USA 85, 7182-7186; Streuli, M. et al.,(1988) J. Exp. Med. 168, 1523-2530; Streuli, M. et al., (1989) Proc.Natl. Acad. Sci. USA 86, 8698-8702). The present inventors havetherefore concluded that ligands in the extracellular environment cancontrol the activity of this membrane-associated subclass of PTPases.

RPTPα and the other RPTPs of the present invention are useful in methodsfor screening drugs and other agents which are capable of activating orinhibiting the RPTP activity, and thereby affecting major pathways ofcellular metabolism. By attaching an intact RPTP, or the ligand-bindingportion thereof, to a solid phase matrix, an affinity probe is createdwhich can be used to screen biological products or chemical agents fortheir capacity to interact with the receptor on the basis of theirbinding activity. Bound material can then be eluted from the affinityprobe in purified form.

Methods for coupling proteins and peptides to the solid phase, the solidphase substances useful in these methods, and means for elution, arewell known to those of skill in the art.

The RPTP protein or derivatives thereof having enzymatic activity can beused for testing of compounds capable of enhancing or inhibiting thephosphatase activity. The ability of a compound under test to modifyphosphatase activity can be tested in an in vitro system wherein thetest compound is added to purified RPTP protein or enzymatically activederivatives thereof, and the affects on enzyme activity measured usingstandard enzymological procedures well known to those of skill in theart.

Alternatively, the action of a compound on RPTP activity can be measuredin a whole cell preparation using live or fixed cells, or a membranefraction derived from live or fixed cells. This method is useful forscreening compounds acting via the extracellular receptor portion of theprotein, as well as compounds acting directly on the enzymatic portionof the protein. A test compound is incubated with cells, or with amembrane preparation derived therefrom, which express high amounts ofthe RPTP of this invention, such as transfected COS or NIH-3T3 cells.The amount of cellular phosphotyrosine is then measured, using methodswell-known in the art (Honegger, A. M. et al., Cell 51:199-209 (1987);Margolis, B. et al., Cell 57:1101-1107 (1989)). The results are comparedto results obtained in the absence of the test compound, or in theabsence or presence of a known activator of RPTP enzymatic activity. Insuch studies, the action of the test compound in the presence of anactivator of tyrosine kinase can also be measured.

A compound which stimulates RPTP activity will result in a net decreasein the amount of phosphotyrosine, whereas a compound which inhibits RPTPactivity will result in a net increase in the amount of phosphotyrosine.

In the case of growth factor receptors which are tyrosine kinases, suchas the receptors for epidermal growth factor (EGF) and forplatelet-derived growth factor (PDGF), tyrosine phosphorylation islinked to cell growth and to oncogenic transformation. Activation of aPTPase, leading to dephosphorylation, would serve as a counterregulatorymechanism to prevent or inhibit growth, and might serve as an endogenousregulatory mechanism against cancer. Thus, mutation or dysregulation ofthis receptor/enzyme system may promote susceptibility to cancer

The insulin receptor is also a tyrosine kinase, and phosphorylation oftyrosine in cells bearing insulin receptors would be associated withnormal physiological function. In contrast to the case of cell growthand cancer, activation of an RPTP would counteract insulin effects.Subnormal RPTP levels or enzymatic activity would act to remove a normalcounterregulatory mechanisms. Perhaps more important, though,over-activity, or inappropriate activation, of a RPTP would be expectedto inhibit or totally prevent the action of insulin on cells, leading todiabetes (of an insulin-resistant variety). Thus, susceptibility todiabetes may be associated with RPTP dysregulation.

Therefore, the methods of the present invention for identifying normalor mutant RPTP genes, or for measuring the amount or activity of RPTPassociated with a cell or tissue, can serve as methods for identifyingsusceptibility to cancer, diabetes, or other diseases associated withalterations in cellular phosphotyrosine metabolism.

The present invention provides methods for evaluating the presence andthe level of normal or mutant RPTP in a subject. Absence, or moretypically, low expression of the RPTP, or presence of a mutant RPTP, inan individual may serve as an important predictor of susceptibility tooncogenic transformation and the development of cancer. Alternatively,over-expression of RPTP, possibly due to a mutant receptor/enzyme systeminsensitive to negative regulation, or due to overabundance of astimulatory ligand in the body, may serve as an important predictor ofsusceptibility to diabetes.

Oligonucleotide probes encoding various portions of the RPTP (see below)are used to test cells from a subject for the presence DNA or RNAsequences encoding the RPTP. A preferred probe would be one directed tothe nucleic acid sequence encoding at least 4 amino acid residues, andpreferably at least 5 amino acid residues, of the RPTPα or other RPTPprotein of the present invention. Qualitative or quantitative assays canbe performed using such probes. For example, Northern analysis (seeExamples III and VI, below) is used to measure expression of an RPTPmRNA in a cell or tissue preparation.

Such methods can be used even with very small amounts of DNA obtainedfrom an individual, following use of selective amplification techniques.Recombinant DNA methodologies capable of amplifying purified nucleicacid fragments have long been recognized. Typically, such methodologiesinvolve the introduction of the nucleic acid fragment into a DNA or RNAvector, the clonal amplification of the vector, and the recovery of theamplified nucleic acid fragment. Examples of such methodologies areprovided by Cohen et al. (U.S. Pat. No. 4,237,224), Sambrook et al.Molecular Cloning: A Laboratory Manual, Second Edition, Cold SpringHarbor Press, Cold Spring Harbor, N.Y. (1989), which references areherein incorporated by reference).

Recently, an in vitro, enzymatic method has been described which iscapable of increasing the concentration of such desired nucleic acidmolecules. This method has been referred to as the “polymerase chainreaction or “PCR” (Mullis, K. et al., Cold Spring Harbor Symp. Quant.Biol. 51:263-273 (1986); Erlich, H. et al., EP 50,424; EP 84,796, EP258,017, EP 237,362; Mullis, K., EP 201,184; Mullis, K. et al., U.S.Pat. No. 4,683,202; Erlich, H., U.S. Pat. No. 4,582,788; and Saiki, R.et al., U.S. Pat. No. 4,683,194).

The polymerase chain reaction provides a method for selectivelyincreasing the concentration of a particular nucleic acid sequence evenwhen that sequence has not been previously purified and is present onlyin a single copy in a particular sample. The method can be used toamplify either single- or double-stranded DNA. The essence of the methodinvolves the use of two oligonucleotide probes to serve as primers forthe template-dependent, polymerase mediated replication of a desirednucleic acid molecule.

The precise nature of the two oligonucleotide probes of the PCR methodis critical to the success off the method. As is well known, a moleculeof DNA or RNA possesses directionality, which is conferred through the5′-3′ linkage of the phosphate groups of the molecule. Sequences of DNAor RNA are linked together through the formation of a phosphodiesterbond between the terminal 5′ phosphate group of one sequence and theterminal 3′ hydroxyl group of a second sequence. Polymerase dependentamplification of a nucleic acid molecule proceeds by the addition of a5′ nucleotide triphosphate to the 3′ hydroxyl end of a nucleic acidmolecule. Thus, the action of a polymerase extends the 3′ end of anucleic acid molecule. These inherent properties are exploited in theselection of the oligonucleotide probes of the PCR. The oligonucleotidesequences of the probes of the PCR method are selected such that theycontain sequences identical to, or complementary to, sequences whichflank the particular nucleic acid sequence whose amplification isdesired.

More specifically, the oligonucleotide sequences of the “first” probe isselected such that it is capable of hybridizing to an oligonucleotidesequence located 3′ to the desired sequence, whereas the oligonucleotidesequence of the “second” probe is selected such that it contains anoligonucleotide sequence identical to one present 5′ to the desiredregion. Both probes possess 3′ hydroxy groups, and therefore can serveas primers for nucleic acid, synthesis.

In the PCR, the reaction conditions are cycled, between those conduciveto hybridization and nucleic acid polymerization, and those which resultin the denaturation of duplex molecules. In the first step of thereaction, the nucleic acids of the sample are transiently heated, andthen cooled, in order to denature any double-stranded molecules whichmay be present. The “first” and “second” probes are then added to thesample at a concentration which greatly exceeds that of the desirednucleic acid molecule. When the sample is incubated under conditionsconducive to hybridization and polymerization, the “first” probe willhybridize to the nucleic acid molecule of the sample at a position 3′ tothe sequence to be amplified. If the nucleic acid molecule of the samplewas initially double-stranded, the “second” probe will hybridize to thecomplementary strand of the nucleic acid molecule at a position 3′ tothe sequence which is the complement of the sequence whose amplificationis desired. Upon addition of a polymerase, the 3′ ends of the “first”and (if the nucleic acid molecule was double-stranded) “second” probeswill be extended. The extension of the “first” probe will result in thesynthesis of an oligonucleotide having the exact sequence of the desirednucleic acid. Extension of the “second” probe will result in thesynthesis of an oligonucleotide having the exact sequence of thecomplement of the desired nucleic acid.

The PCR reaction is capable of exponential amplification of specificnucleic acid sequences because the extension product of the “first”probe, of necessity, contains a sequence which is complementary to asequence of the “second” probe, and thus can serve as a template for theproduction of an extension product of the “second” probe. Similarly, theextension product of the “second” probe, of necessity, contains asequence which is complementary to a sequence of the “first” probe, andthus can serve as a template for the production of an extension productof the “first” probe. Thus, by permitting cycles of polymerization, anddenaturation, a geometric increase in the concentration of the desirednucleic acid molecule can be achieved. Reviews of the PCR are providedby Mullis, K. B. (Cold Spring Harbor Symp. Quant. Biol. 51:263-273(1986)); Saiki, R. K., et al. (Bio/Technology 3:1008-1012 (1985)); andMullis, K. B., et al. (Meth. Enzymol. 155:335-350 (1987)).

In one embodiment, the invention is directed to a naturally occurringmammalian RPTPα. In another embodiment, the invention is directed to arecombinant mammalian RPTPα. The preferred RPTPs of the presentinvention are of human origin. The invention provides the naturallyoccurring molecule substantially free of other proteins with which it isnatively associated. “Substantially free of other proteins orglycoproteins” indicates that the protein has been purified away from atleast 90 percent (on a weight basis), and from even at least 99 percentif desired, of other proteins and glycoproteins with which it isnatively associated, and is therefore substantially free of them. Thatcan be achieved by subjecting the cells, tissue or fluids containing theRPTP to standard protein purification techniques such as immunoadsorbentcolumns bearing monoclonal antibodies reactive against the protein.Other forms of affinity purification can utilize solid-phase substrateswhich can bind the PTPase domain, or a ligand that will bind to thereceptor domain. Alternatively, the purification can be achieved by acombination of standard methods, such as ammonium sulfate precipitation,molecular sieve chromatography, and ion exchange chromatography.

It will be understood that the mammalian RPTP of the present inventioncan be biochemically purified from a variety of cell or tissue sources.For preparation of naturally occurring RPTP, tissues such as mammalianplacenta or brain, especially of human origin, are preferred.

Alternatively, because the gene for the RPTP can be isolated orsynthesized, the polypeptide can be synthesized substantially free ofother proteins or glycoproteins of mammalian origin in a prokaryoticorganism or in a non-mammalian eukaryotic organism, if desired. Asintended by the present invention, a recombinant RPTPα molecule producedin mammalian cells, such as transfected COS, NIH-3T3, or CHO cells, forexample, is either a naturally occurring protein sequence areafunctional derivative thereof. Where a naturally occurring protein orglycoprotein is produced by recombinant means, it is providedsubstantially free of the other proteins and glycoproteins with which itis natively associated.

Alternatively, methods are well known for the synthesis of polypeptidesof desired sequence on solid phase supports and, their subsequentseparation from the support.

In a further embodiment, the invention provides “functional derivatives”of the RPTP. By “functional, derivative” is meant a “fragment,”“variant,” “analog,” or “chemical derivative” of the RPTP, which termsare defined below. A function al derivative retains at least a portionof the function of the RPTP, such as binding to a specific antibody,phosphatase enzymatic activity or binding of the extracellular domain toa ligand, which permits its utility in accordance with the presentinvention.

A “fragment” of the RPTP refers to any subset of the molecule, that is,a shorter peptide.

A “variant” of the RPTP refers to a molecule substantially similar toeither the entire peptide or a fragment thereof. Variant peptides may beconveniently prepared by direct chemical synthesis of the variantpeptide, using methods well-known in the art.

Alternatively, amino acid sequence variants of the peptide can beprepared by mutations in the DNA which encodes the synthesized peptide.Such variants include, for example, deletions from, or insertions orsubstitutions of, residues within the amino acid sequence. Anycombination of deletion, insertion, and substitution may also be made toarrive at the final construct, provided that the final constructpossesses the desired activity. Obviously, the mutations that will bemade in the DNA encoding the variant peptide must not alter the readingframe and preferably will, not create complementary regions that couldproduce secondary mRNA structure (see European Patent Publication No. EP75,444).

At the genetic level, these variants ordinarily are prepared bysite-directed mutagenesis (as exemplified by Adelman et al., DNA 2:183(1983)) of nucleotides in the DNA encoding the peptide molecule, therebyproducing DNA encoding the variant, and thereafter expressing the DNA inrecombinant cell culture (see below). The variants typically exhibit thesame qualitative biological activity as the nonvariant peptide.

An “analog” of the RPTP refers to a non-natural molecule substantiallysimilar to either the entire molecule or a fragment thereof.

A “chemical derivative” of the RPTP contains additional chemicalmoieties not normally a part of the peptide. Covalent modifications ofthe peptide are included within the scope of this invention. Suchmodifications may be introduced into the molecule by reacting targetedamino acid residues of the peptide with an organic derivatizing agentthat is capable of reacting with selected side chains or terminalresidues.

Cysteinyl residues most commonly are reacted with alpha-haloacetates(and corresponding amines), such as chloroacetic acid orchloroacetamide, to give carboxymethyl or carboxyamidomethylderivatives. Cysteinyl residues also are derivatized by reaction withbromotrifluoroacetone, alpha-bromo-beta-(5-imidozoyl)propionic acid,chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide,methyl 2-pyridyl disulfide, p-chloromercuribenzoate,2-chloromercuri-4-nitrophenol, or chloro-7-nitrobenzo-2-oxa-1,3-diazole.

Histidyl residues are derivatized by reaction with diethylprocarbonateat pH 5.5-7.0 because this agent is relatively specific for the histidylside chain. Para-bromophenacyl bromide also is useful; the reaction ispreferably performed in 0.1 M sodium cacodylate at pH 6.0.

Lysinyl and amino terminal residues are reacted with succinic or othercarboxylic acid anhydrides. Derivatization with these agents has theeffect of reversing the charge of the lysinyl residues. Other suitablereagents for derivatizing alpha-amino-containing residues includeimidoesters such as methyl picolinimidate; pyridoxal phosphate;pyridoxal; chloroborohydride; trinitrobenzenesulfonic acid;O-methylisourea; 2,4 pentanedione; and transaminase-catalyzed reactionwith glyoxylate.

Arginyl residues are modified by reaction with one or severalconventional reagents, among them phenylglyoxal, 2,3-butanedione,1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residuesrequires that the reaction be performed in alkaline conditions becauseof the high pK_(a) of the guanidine functional group. Furthermore, thesereagents may react with the groups of lysine as well as the arginineepsilon-amino group.

The specific modification of tyrosyl residues per se has been studiedextensively, with particular interest in introducing spectral labelsinto tyrosyl residues by reaction with aromatic diazonium compounds ortetranitromethane. Most commonly, N-acetylimidizol sandtetranitromethane are used to form O-acetyl tyrosyl species and 3-nitroderivatives, respectively.

Carboxyl side groups (aspartyl or glutamyl) are selectively modified byreaction with carbodiimides (R′—N—C—N—R′) such as1-cyclohexyl-3-(2-morpholinyl-(4-ethyl) carbodiimide or1-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide. Furthermore,aspartyl and glutamyl residues are converted to asparaginyl andglutaminyl residues by reaction with ammonium ions.

Glutaminyl and asparaginyl residues are frequently deamidated to thecorresponding glutamyl and aspartyl residues. Alternatively, theseresidues are deamidated under mildly acidic conditions. Either form ofthese residues falls within the scope of this invention.

Derivatization with bifunctional agents is useful for cross-linking thepeptide to a water-insoluble support matrix or to other macromolecularcarriers. Commonly used cross-linking agents include, e.g.,1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylicacid, homobifunctional imidoesters, including disuccinimidyl esters suchas 3,3′-dithiobis(succinimidyl-propionate), and bifunctional maleimidessuch as bis-N-maleimido-1,8-octane. Derivatizing agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate yield photoactivatableintermediates that are capable of forming crosslinks in the presence oflight. Alternatively, reactive water-insoluble matrices such as cyanogenbromide-activated carbohydrates and the reactive substrates described inU.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537;and 4,330,440 are employed for protein immobilization.

Other modifications include hydroxylation of proline and lysine,phosphorylation of hydroxyl groups of seryl or threonyl residues,methylation of the alpha-amino groups of lysine, arginine, and histidineside chains (T. E. Creighton, Proteins: Structure and MoleculeProperties, W.H. Freeman & Co., San Francisco, pp. 79-86 (1983.)),acetylation of the N-terminal amine, and, in some instances, amidationof the C-terminal carboxyl groups.

Such derivatized moieties may improve the solubility, absorption,biological half life, and the like. The moieties may alternativelyeliminate or attenuate any undesirable side effect of the protein andthe like. Moieties capable of mediating such effects are disclosed, forexample, in Remington's Pharmaceutical Sciences, 16th ed., MackPublishing Co., Easton, Pa. (1980)

This invention is also directed to an antibody specific for an epitopeof RPTP, preferably, of RPTPα, most preferably of human RPTPα, and theuse of such antibody to detect the presence of, or measure the quantityor concentration of, the RPTP in a cell, a cell or tissue extract, or abiological fluid.

The term “antibody” is meant to include polyclonal antibodies,monoclonal antibodies (mAbs), chimeric antibodies, and anti-idiotypic(anti-Id) antibodies.

Polyclonal antibodies are heterogeneous populations of antibodymolecules derived from the sera of animals immunized with an antigen.

Monoclonal antibodies are a substantially homogeneous population ofantibodies to specific antigens. MAbs may be obtained by methods knownto those skilled in the art. See, for example Kohler and Milstein,Nature 256:495-497 (1975) and U.S. Pat. No. 4,376,110. Such antibodiesmay be of any immunoglobulin class including IgG, IgM, IgE, IgA, GILDand any subclass thereof. The hybridoma producing the mAbs of thisinvention may be cultivated in vitro or in vivo. Production of hightiters of mAbs in vivo production makes this the presently preferredmethod of production. Briefly, cells from the individual hybridomas areinjected intraperitoneally into pristane-primed BALB/c mice to produceascites fluid containing high concentrations of the desired mAbs. MAbsof isotype IgM or IgG may be purified from such ascites fluids, or fromculture supernatants, using column chromatography methods well known tothose of skill in the art.

Chimeric antibodies are molecules different portions of which arederived from different animal species, such as those having variableregion derived from a murine mAb and a human immunoglobulin constantregion. Chimeric antibodies and methods for their production are knownin the art (Cabilly et al, Proc. Natl. Acad. Sci. USA 81:3273-3277(1984); Morrison et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984);Boulianne et al., Nature 312:643-646 (1984); Cabilly et al., EuropeanPatent Application 125023 (published Nov. 14, 1984); Neuberger et al.,Nature 314:268-270 (1985); Taniguchi et al., European Patent Application171496 (published Feb. 19, 1985); Morrison et al., European PatentApplication 173494 (published Mar. 5, 1986); Neuberger et al., PCTApplication WO 86/01533 (published Mar. 13, 1986); Kudo et al., EuropeanPatent Application 184187 (published Jun. 11, 1986); Morrison et al.,European Patent Application 173494 (published Mar. 5, 1986); Sahagan etal., J. Immunol. 137:1066-1074 (1986); Robinson et al., InternationalPatent Publication #PCT/US86/02269 (published 7 May 1987); Liu et al.,Proc. Natl. Acad. Sci. USA 84:3439-3443 (1987); Sun et al., Proc. Natl.Acad. Sci. USA 84:214-218 (1987); Better et al., Science 240:1041-1043(1988)). These references are hereby incorporated by reference.

An anti-idiotypic (anti-Id) antibody is an antibody which recognizesunique determinants generally associated with the antigen-binding siteof an antibody. An anti-Id antibody can be prepared by immunizing ananimal of the same species and genetic type (e.g. mouse strain) as thesource of the mAb with the mAb to which an anti-Id is being prepared.The immunized animal will recognize and respond to the idiotypicdeterminants of the immunizing antibody by producing an antibody tothese idiotypic determinants (the anti-Id antibody).

The anti-Id antibody may also be used as an “immunogen” to induce animmune response in yet another animal, producing a so-calledanti-anti-Id antibody. The anti-anti-Id may be epitopically identical tothe original mAb which induced the anti-Id. Thus, by using antibodies tothe idiotypic determinants of a mAb, it is possible to identify otherclones expressing antibodies of identical specificity.

Accordingly, mAbs generated against the RPTP of the present inventionmay be used to induce anti-Id antibodies in suitable animals, such asBALB/c mice. Spleen cells from such immunized mice are used to produceanti-Id hybridomas secreting anti-Id mAbs. Further, the anti-Id mAbs canbe coupled to a carrier such as keyhole limpet hemocyanin (KLH) and usedto immunize additional BALB/c mice. Sera from these mice will containanti-anti-Id antibodies that have the binding properties of the originalmAb specific for a RPTP epitope.

The anti-Id mAbs thus have their own idiotypic epitopes, or “idiotopes”structurally similar to the epitope being evaluated, such as RPTPα.

The term “antibody” is also meant to include both intact molecules aswell as fragments thereof, such as, for example, Fab and F(ab′)₂, whichare capable of binding antigen. Fab and F(ab′)₂ fragments lack the Fcfragment of intact antibody, clear more rapidly from the circulation,and may have less non-specific tissue binding than an intact antibody(Wahl et al., J. Nucl. Med. 24:316-325 (1983)).

It will be appreciated that Fab and F(ab′)₂ and other fragments of theantibodies useful in the present invention may be used for the detectionand quantitation of RPTP according to the methods disclosed herein forintact antibody molecules. Such fragments are typically produced byproteolytic cleavage, using enzymes such as papain (to produce Fabfragments) or pepsin (to produce F(ab′)₂ fragments).

An antibody is said to be “capable of binding” a molecule if it iscapable of specifically reacting with the molecule to thereby bind themolecule to the antibody. The term “epitope” is meant to refer to thatportion of any molecule capable of being bound by an antibody which canalso be recognized by that antibody. Epitopes or “antigenicdeterminants” usually consist of chemically active surface groupings ofmolecules such as amino acids or sugar side chains and have specificthree dimensional structural characteristics as well as specific chargecharacteristics.

An “antigen” is a molecule or a portion of a molecule capable of beingbound by an antibody which is additionally capable of inducing an animalto produce antibody capable of binding to an epitope of that antigen. Anantigen may have one, or more than one epitope. The specific reactionreferred to above is meant to indicate that the antigen will react, in ahighly selective manner, with its corresponding antibody and not withthe multitude of other antibodies which may be evoked by other antigens.

The antibodies, or fragments of antibodies, useful in the presentinvention may be used to quantitatively or qualitatively detect thepresence of cells which express the RPTP protein. This can beaccomplished by immunofluorescence techniques employing a fluorescentlylabeled antibody (see below) coupled with light microscopic, flowcytometric, or fluorimetric detection.

The antibodies (of fragments thereof) useful in the present inventionmay be employed histologically, as in immunofluorescence orimmunoelectron microscopy, for in situ detection of RPTP. In situdetection may be accomplished by removing a histological specimen from apatient, and providing the a labeled antibody of the present inventionto such a specimen. The antibody (or fragment) is preferably provided byapplying or by overlaying the labeled antibody (or fragment) to abiological sample. Through the use of such a procedure, it is possibleto determine not only the presence of the RPTP but also its distributionon the examined tissue. Using the present invention, those of ordinaryskill will readily perceive that any of a wide variety of histologicalmethods (such as staining procedures) can be modified in order toachieve such in situ detection. Such assays for RPTP typically comprisesincubating a biological sample, such as a biological fluid, a tissueextract, freshly harvested cells such as lymphocytes or leucocytes, orcells which have been incubated in tissue culture, in the presence of adetectably labeled antibody capable of identifying RPTP, and detectingthe antibody by any of a number of techniques well-known in the art.

The biological sample may be treated with a solid phase support such asnitrocellulose, or other solid support which is capable of immobilizingcells, cell particles or soluble proteins. The support may then bewashed with suitable buffers followed by treatment with the detectablylabeled RPTP-specific antibody. The solid phase support may then bewashed with the buffer a second time to remove unbound antibody. Theamount of bound label on said solid support may then be detected byconventional means.

By “solid phase support” is intended any support capable of bindingantigen or antibodies. Well-known supports, or carriers, include glass,polystyrene, polypropylene, polyethylene, dextran, nylon, amylases,natural and modified celluloses, polyacrylamides, gabbros, andmagnetite. The nature of the carrier can be either soluble to someextent or insoluble for the purposes of the present invention. Thesupport material may have virtually any possible structuralconfiguration so long as the coupled molecule is capable of binding toan antigen or antibody. Thus, the support configuration may bespherical, as in a bead, or cylindrical, as in the inside surface of atest tube, or the external surface of a rod. Alternatively, the surfacemay be flat such as a sheet, test strip, etc. Preferred supports includepolystyrene beads. Those skilled in the art will know many othersuitable carriers for binding antibody or antigen, or will be able toascertain the same by use of routine experimentation.

The binding activity of a given lot of anti-RPTP antibody may bedetermined according to well known methods. Those skilled in the artwill be able to determine operative and optimal assay conditions foreach determination by employing routine experimentation.

Other such steps as washing, stirring, shaking, filtering and the likemay be added to the assays as is customary or necessary for theparticular situation.

One of the ways in which the RPTP-specific antibody can be detectablylabeled is by linking the same to an enzyme and use in an enzymeimmunoassay (EIA). This enzyme, in turn, when later exposed to anappropriate substrate, will react with the substrate in such a manner asto produce a chemical moiety which can be detected, for example, byspectrophotometric, fluorimetric or by visual means. Enzymes which canbe used to detectably label the antibody include, but are not limitedto, malate dehydrogenase, staphylococcal nuclease, delta-5-steroidisomerase, yeast alcohol dehydrogenase, alpha-glycerophosphatedehydrogenase, triose phosphate isomerase, horseradish peroxidase,alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase,ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase,glucoamylase and acetylcholinesterase. The detection can be accomplishedby colorimetric methods which employ a chromogenic substrate for theenzyme. Detection may also be accomplished by visual comparison of theextent of enzymatic reaction of a substrate in comparison with similarlyprepared standards.

Detection may be accomplished using any of a variety of otherimmunoassays. For example, by radioactively labeling the antibodies orantibody fragments, it is possible to detect an RPTP through the use ofa radioimmunoassay (RIA) (see, for example, Work, T. S. et al.,Laboratory Techniques and Biochemistry in Molecular Biology, NorthHolland Publishing Company, New York, 1978, which is incorporated byreference herein). The radioactive isotope can be detected by such meansas the use of a gamma counter or a scintillation counter or byautoradiography.

It is also possible to label the antibody with a fluorescent compound.When the fluorescently labeled antibody is exposed to light of theproper wave length, its presence can then be detected due tofluorescence. Among the most commonly used fluorescent labellingcompounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.

The antibody can also be detectably labeled using fluorescence emittingmetals such as ¹⁵²Eu, or others of the lanthanide series. These metalscan be attached to the antibody using such metal chelating groups asdiethylenetriaminepentaacetic acid (DTPα) or ethylenediaminetetraaceticacid (EDTA).

The antibody also can be detectably labeled by coupling it to achemiluminescent compound. The presence of the chemiluminescent-taggedantibody is then determined by detecting the presence of luminescencethat arises during the course of a chemical reaction. Examples ofparticularly useful chemiluminescent labeling compounds are luminol,isoluminol, theromatic acridinium ester, imidazole, acridinium salt andoxalate ester.

Likewise, a bioluminescent compound may be used to label the antibody ofthe present invention. Bioluminescence is a type of chemiluminescencefound in biological systems in which a catalytic protein increases theefficiency of the chemiluminescent reaction. The presence of abioluminescent protein is determined by detecting the presence ofluminescence Important bioluminescent compounds for purposes of labelingare luciferin, luciferase and aequorin.

The antibody molecules of the present invention may be adapted forutilization in an immunometric assay, also known as a “two-site” or“sandwich” assay. In a typical immunometric assay, a quantity ofunlabeled antibody (or fragment of antibody) is bound to a solid supportand a quantity of detectably labeled soluble antibody is added to permitdetection and/or quantitation of the ternary complex formed betweensolid-phase antibody, antigen, and labeled antibody.

Typical, and preferred, immunometric assays include “forward” assays inwhich the antibody bound to the solid phase is first contacted with thesample being tested to extract the antigen from the sample by formationof a binary solid phase antibody-antigen complex. After a suitableincubation period, the solid support is washed to remove the residue ofthe fluid sample, including unreacted antigen, if any, and thencontacted with the solution containing an unknown quantity of labeledantibody (which functions as a “reporter molecule”). After a secondincubation period to permit the labeled antibody to complex with theantigen bound to the solid support through the unlabeled antibody, thesolid support is washed a second time to remove the unreacted labeledantibody.

In another type of “sandwich” assay, which may also be useful with theantigens of the present invention, the so-called “simultaneous” and“reverse” assays are used. A simultaneous assay involves a singleincubation step as the antibody bound to the solid support and labeledantibody are both added to the sample being tested at the same time.After the incubation is completed, the solid support is washed to removethe residue of fluid sample and uncomplexed labeled antibody. Thepresence of labeled antibody associated with the solid support is thendetermined as it would be in a conventional “forward” sandwich assay.

In the “reverse” assay, stepwise addition first of a solution of labeledantibody to the fluid sample followed by the addition of unlabeledantibody bound to a solid support after a suitable incubation period isutilized. After a second incubation, the solid phase is washed inconventional fashion to free it of the residue of the sample beingtested and the solution of unreacted labeled antibody. The determinationof labeled antibody associated with a solid support is then determinedas in the “simultaneous” and “forward” assays.

The presence of normally functioning RPTP in a subject can also betested using direct enzymatic assays, for the tyrosine phosphataseactivity. Such biochemical measurements can be performed in vitro, usingpurified enzymes, allowing precise measurements of enzyme activity, orwith membrane preparations, or whole cells, where the netphosphotyrosine level is determined.

In additional embodiments of the present invention, a DNA sequenceencoding a RPTP molecule and methods for expressing the DNA sequence areprovided. One of ordinary skill in the art will know how to identify andclone additional RPTP molecules, of human or other mammalian species,which have sequence homology to the RPTP molecules described herein,using the genetic sequences and oligonucleotides of the presentinvention without undue experimentation. Furthermore, manipulation ofthe genetic constructs of the present invention allow the grafting of aparticular ligand-binding receptor domain onto the transmembrane andcatalytic portions of the RPTP resulting in chimeric molecules.Non-limiting examples of such chimeric molecules include the RPTPwherein the receptor is an epidermal growth factor receptor, afibroblast growth factor receptor, and the like. Genetically engineeredchimeric receptors are known in the art (see, for example, Riedel, H. etal., Nature 324:628-670 (1986)).

Genetic constructs encoding RPTPα, functional derivative thereof, andchimeric molecules such as those described above, can be used in genetherapy. An abnormal or dysfunctional RPTP, which results in disease,may be replaced by infusion of cells of the desired lineage (such ashemopoietic cells, for example) transfected with a normal RPTP.Alternatively, or additionally, cells carrying a chimeric RPTP having areceptor to a ligand of choice (e.g. EGF) can be used for such genetherapy.

The recombinant DNA molecules of the present invention can be producedthrough any of a variety of means, such as, for example, DNA or RNAsynthesis, or more preferably, by application of recombinant DNAtechniques. Techniques for synthesizing such molecules are disclosed by,for example, Wu, R., et al. (Prop. Nucl. Acid. Res. Molec. Biol.21:101-141 (1978)). Procedures for constructing recombinant molecules inaccordance with the above-described method are disclosed by Sambrook etal. (supra).

The 3′ terminus of the recombinant molecule of this invention ispreferably treated to render it unsuitable for polymerization. Suchtreatment may be accomplished by blocking the terminus by chemicalmeans, or by modifying the terminal bases such that they stericallyinterfere with polymerase action. In a preferred embodiment, suchtreatment is accomplished by immobilizing the 3′ terminus, such as bycoupling it to a solid support (such as, for example, glass, plastic,latex, etc.). The support may be of any form (i.e. a sheet, rod, sphere,ovoid, etc. Procedures for such immobilization are well known to thoseof ordinary skill. In the most preferred embodiment, the 3′ end of therecombinant molecule is covalently bound to the solid support. A spacerregion may be used to extend the probe outward from the solid support aslong as (1) it will not sterically hinder any function or characteristicof the recombinant molecule, and (2) the sequence of the spacer regiondoes not participate in the hybridization or polymerization reactions ofthe assay. It is typically desirable to, immobilize several, andpreferably, a large number of such recombinant molecule to the support.

Oligonucleotides representing a portion of an RPTP are useful forscreening for the presence of genes encoding such proteins and for thecloning of RPTP genes. Techniques for synthesizing such oligonucleotidesare disclosed by, for example, Wu, R., et al., Prop. Nucl. Acid. Res.Molec. Biol. 21:101-141 (1978)).

Protein molecules are fragmented as with cyanogen bromide, or withproteases such as papain, chymotrypsin, trypsin, etc. (Oike, Y., et al.,J. Biol. Chem. 257:9751-9758 (1982); Liu, C., et al., Int. J. Pent.Protein Res. 21:209-215 (1983)). Because the genetic code is degenerate,more than one codon may be used to encode a particular amino acid(Watson, J. D., In: Molecular Biology of the Gene, 4th Ed.,Benjamin/Cummings Publishing Co., Inc., Menlo Park, Calif. (1987)).Using the genetic code, one or more different oligonucleotides can beidentified, each of which would be capable of encoding the amino acid.The probability that a particular oligonucleotide will, in fact,constitute the actual XXX-encoding sequence can be estimated byconsidering abnormal base pairing relationships and the frequency withwhich a particular codon is actually used (to encode a particular aminoacid) in eukaryotic cells. Such “codon usage rules” are disclosed byLathe, R., et al., J. Molec. Biol. 183:1-12 (1985). Using the “codonusage rules” of Lathe, a single oligonucleotide, or a set ofoligonucleotides, that contains a theoretical “most probable” nucleotidesequence capable of encoding the RPTP sequences is identified.

Although occasionally an amino acid sequences may be encoded by only asingle oligonucleotide frequently the amino acid sequence may be encodedby, any of a set of similar oligonucleotides. Importantly, whereas allof the members of this set contain oligonucleotides which are capable ofencoding the peptide fragment and, thus, potentially contain the sameoligonucleotide sequence as the gene which encodes the peptide fragment,only one member of the set contains the nucleotide sequence that isidentical to the nucleotide sequence of the gene. Because this member ispresent within the set, and is capable of hybridizing to DNA even in thepresence of the other members of the set, it is possible to employ theunfractionated set of oligonucleotides in the same manner in which onewould employ a single oligonucleotide to clone the gene that encodes thepeptide.

The oligonucleotide, or set of oligonucleotides, containing thetheoretical “most probable” sequence capable of encoding the RPTPfragment is used to identify the sequence of a complementaryoligonucleotide or set of oligonucleotides which is capable ofhybridizing to the “most probable” sequence, or set of sequences. Anoligonucleotide containing such a complementary sequence can be employedas a probe to identify and isolate the RPTP gene (Sambrook et al.,supra).

A suitable oligonucleotide, or set of oligonucleotides, which is capableof encoding a fragment of the RPTP gene (or which is complementary tosuch an oligonucleotide, or set of oligonucleotides) is identified(using the above-described procedure), synthesized, and hybridized bymeans well known in the art, against a DNA or, more preferably, a cDNApreparation derived from cells which are capable of expressing the RPTPgene. Single stranded oligonucleotide molecules complementary to the“most probable” RPTP peptide encoding sequences can be synthesized usingprocedures which are well known to those of ordinary skill in the art(Belagaje, R., et al., J. Biol. Chem. 254:5765-5780 (1979); Maniatis,T., et al., In: Molecular Mechanisms in the Control of Gene Expression,Nierlich, D. P., et al., Eds., Acad. Press, New York (1976); Wu, R., etal., Prog. Nucl. Acid Res. Molec. Biol. 21:101-141 (1978); Khorana, R.G., Science 203:614-625 (1979)). Additionally, DNA synthesis may beachieved through the use of automated synthesizers. Techniques ofnucleic acid hybridization are disclosed by Sambrook et al. (supra), andby Haymes, B. D., et al. (In: Nucleic Acid Hybridization, A PracticalApproach, IRL Press, Washington, D.C. (1985)), which references areherein incorporated by reference. Techniques such as, or similar to,those described above have successfully enabled the cloning of genes forhuman aldehyde dehydrogenases (Hsu, L. C., et al., Proc. Natl. Acad.Sci. USA 82:3771-3775 (1985)), fibronectin (Suzuki, S., et al., EMBO J.4:2519-2524 (1985)), the human estrogen receptor gene (Walter, P., etal., Proc. Natl. Acad. Sci. USA 82:7889-7893 (1985)), tissue-typeplasminogen activator (Pennica, D., et al., Nature 301:214-221 (1983))and human term placental alkaline phosphatase complementary DNA (Kam,W., et al., Proc. Natl. Acad. Sci. USA 82:(715-8719 (1985)).

In a alternative way of cloning the RPTP gene, a library of expressionvectors is prepared by cloning DNA or, more preferably, cDNA (from acell capable of expressing RPTP) into an expression vector. The libraryis then screened for members capable of expressing a protein which bindsto anti-RPTP antibody, and which has a nucleotide sequence that iscapable of encoding polypeptides that have the same amino acid sequenceas RPTP, or fragments thereof. In this embodiment, DNA, or morepreferably cDNA, is extracted and purified from a cell which is capableof expressing RPTP protein. The purified cDNA is fragmented (byshearing, endonuclease digestion, etc.) to produce a pool of DNA or cDNAfragments. DNA or cDNA fragments from this pool are then cloned into anexpression vector in order to produce a genomic library of expressionvectors whose members each contain a unique cloned DNA or cDNA fragment.

An “expression vector” is a vector which (due to the presence ofappropriate transcriptional and/or translational control sequences) iscapable of expressing a DNA (or cDNA) molecule which has been clonedinto the vector and of thereby producing a polypeptide or protein.Expression of the cloned sequences occurs when the expression vector isintroduced into an appropriate host cell. If a prokaryotic expressionvector is employed, then the appropriate host cell would be anyprokaryotic cell capable of expressing the cloned sequences. Similarly,if a eukaryotic expression vector is employed, then the appropriate hostcell would be any eukaryotic cell capable of expressing the clonedsequences. Importantly, since eukaryotic DNA may contain interveningsequences, and since such sequences cannot be correct ly processed inprokaryotic cells, it is preferable to employ cDNA from a cell which iscapable of expressing RPTP in order to produce a prokaryotic genomicexpression vector library. Procedures for preparing cDNA and forproducing a genomic library are disclosed by Sambrook et al. (supra).

A DNA sequence encoding the RPTP of the present invention, or itsfunctional derivatives, may be recombined with vector DNA in accordancewith conventional techniques, including blunt-ended or staggered-endedtermini for ligation, restriction enzyme digestion to provideappropriate termini, filling in of cohesive ends as appropriate,alkaline phosphatase treatment to avoid undesirable joining, andligation with appropriate ligases. Techniques for such manipulations aredisclosed by Sambrook et al., supra, and are well known in the art.

A nucleic acid molecule, such as DNA, is said to be “capable ofexpressing” a polypeptide if it contains nucleotide sequences whichcontain transcriptional and translational regulatory information andsuch sequences are “operably linked” to nucleotide sequences whichencode the polypeptide. An operable linkage is a linkage in which theregulatory DNA sequences and the DNA sequence sought to be expressed areconnected in such a way as to permit gene expression. The precise natureof the regulatory regions needed for gene expression may vary fromorganism to organism, but shall in general include a promoter regionwhich, in prokaryotes, contains both the promoter (which directs theinitiation of RNA transcription) as well as the DNA sequences which,when transcribed into RNA, will signal the initiation of proteinsynthesis. Such regions will normally include those 5′-non-codingsequences involved with initiation of transcription and translation,such as the TATA box, capping sequence, CAAT sequence, and the like.

If desired, the non-coding region 3′ to the gene sequence coding for theprotein may be obtained by the above-described methods. This region maybe retained for its transcriptional termination regulatory sequences,such as termination and polyadenylation. Thus, by retaining the3′-region naturally contiguous to the DNA sequence coding for theprotein, the transcriptional termination signals may be provided. Wherethe transcriptional termination signals are not satisfactorilyfunctional in the expression host cell, then a 3′ region functional inthe host cell may be substituted.

Two DNA sequences (such as a promoter region sequence and aRPTP-encoding sequence) are said to be operably linked if the nature ofthe linkage between the two DNA sequences does not (1) result in theintroduction of a frame-shift mutation, (2) interfere with the abilityof the promoter region sequence to direct the transcription of the RPTPgene sequence, or (3) interfere with the ability of the RPTP genesequence to be transcribed by the promoter region sequence. A promoterregion would be operably linked to a DNA sequence if the promoter werecapable of effecting transcription of that DNA sequence. Thus, toexpress the protein, transcriptional and translational signalsrecognized by an appropriate host are necessary.

A promoter is a double-stranded DNA or RNA molecule which is capable ofbinding RNA polymerase and promoting the transcription of an “operablylinked” nucleic acid sequence. As used herein, a “promoter sequence” isthe sequence of the promoter which is found on that strand of the DNA orRNA which is transcribed by the RNA polymerase. A “promoter sequencecomplement” is a nucleic acid molecule whose sequence is the complementof a “promoter sequence.” Hence, upon extension of a primer DNA or RNAadjacent to a single-stranded “promoter sequence complement” or, of a“promoter sequence,” a double-stranded molecule is created which willcontain a functional promoter, if that extension proceeds towards the“promoter sequence” or the “promoter sequence complement.” Thisfunctional promoter will direct the transcription of a nucleic acidmolecule which is operably linked to that strand of the double-strandedmolecule which contains the “promoter sequence” (and not that strand ofthe molecule which contains the “promoter sequence complement”).

Certain RNA polymerases exhibit a high specificity for such promoters.The RNA polymerases of the bacteriophages T7, T3, and SP-6 areespecially well characterized, and exhibit high promoter specificity.The promoter sequences which are specific for each of these RNApolymerases also direct the polymerase to utilize (i.e. transcribe) onlyone strand of the two strands of a duplex DNA template. The selection ofwhich strand is transcribed is determined by the orientation of thepromoter sequence. This selection determines the direction oftranscription since RNA is only polymerized enzymatically by theaddition of a nucleotide 5′ phosphate to a 3′ hydroxyl terminus.

Two sequences of a nucleic acid molecule are said to be “operablylinked” when they are linked to each other in a manner which eitherpermits both sequences to be transcribed onto the same RNA transcript,or permits an RNA transcript, begun in one sequence to be extended intothe second sequence. Thus, two sequences, such as a promoter sequenceand any other “second” sequence of DNA or RNA are operably linked iftranscription commencing in the promoter sequence will produce an RNAtranscript of the operably linked second sequence. In order to be“operably linked” it is not necessary that two sequences be immediatelyadjacent to one another.

Thus, as indicated above, in order to function as a promoter, a promotersequence must be present as a double-stranded molecule. For the purposesof the present invention, the two strands of a functional promotersequence are referred to as a “transcript” strand and a “complementary”strand. The “transcript” strand is that strand of the duplex which willbe transcribed by the RNA polymerase (i.e. which serves as the templatefor transcription). The “complementary” strand is the strand which has asequence complementary to the “transcript” strand, and which must bepresent, and hybridized to the “transcript” strand, in order fortranscription to occur. Thus, when the “transcript” strand of a promotersequence is operably linked to a second sequence, hybridization of the“transcript” strand with the “complement” strand, will, in the presenceof a polymerase, result in the transcription of the “transcript” strand,and will produce an RNA transcript using the sequence of the“transcript” strand as a template.

The promoter sequences of the present invention may be eitherprokaryotic, eukaryotic or viral. Suitable promoters are repressible,or, more preferably, constitutive. Examples of suitable prokaryoticpromoters include promoters capable of recognizing the T4 (Malik, S. etal., J. Biol. Chem. 263:1174-1181 (1984); Rosenberg, A. H. et al., Gene59:191-200 (1987); Shinedling, S. et al., J. Molec. Biol. 195:471-480(1987); Hu, M. et al., Gene 42:21-30 (1986)), T3, Sp6, and T7(Chamberlin, M. et al., Nature 228:227-231 (1970); Bailey, J. N. et al.,Proc. Natl. Acad. Sci. (U.S.A.) 80:2814-2818 (1983); Davanloo, P. etal., Proc. Natl. Acad. Sci. (U.S.A.) 81:2035-2039 (1984)) polymerases;the P_(R) and P_(L) promoters of bacteriophage λ (The BacteriophageLambda, Hershey, A. D., Ed., Cold Spring Harbor Press, Cold SpringHarbor, N.Y. (1973); Lambda II, Hendrix, R. W., Ed., Cold Spring HarborPress, Cold Spring Harbor, N.Y. (1980)); the trp, recA, heat shock, andlacZ promoters of E. coli; the α-amylase (Ulmanen, I., et al., J.Bacteriol. 162:176-182 (1985)) and the σ-28-specific promoters of B.subtilis (Gilman, M. Z., et al., Gene 32:11-20 (1984)); the promoters ofthe bacteriophages of Bacillus (Gryczan, T. J., In: The MolecularBiology of the Bacilli, Academic Press, Inc., New York (1982));Streptomyces promoters (Ward, J. M., et al., Mol. Gen. Genet.203:468-478 (1986)); the int promoter of bacteriophage λ; the blapromoter of the β-lactamase gene of pBR32, and the CAT promoter of thechloramphenicol acetyl transferase gene of pPR325, etc. Prokaryoticpromoters are reviewed by Glick, B. R. (J. Ind. Microbiol. 1:277-282(1987)); Cenatiempo, Y. (Biochimie 68:505-516 (1986)); Watson, J. D. etal. (In: Molecular Biology of the Gene, Fourth Edition, BenjaminCummins, Menlo Park, Calif. (1987)); and Gottesman, S. (Ann. Rev. Genet.18:415-442 (1984)). Preferred eukaryotic promoters include the promoterof the mouse metallothionein I gene (Hamer, D., et al., J. Mol. Appl.Gen. 1:273-288 (1982)); the TK promoter of Herpes virus (McKnight, S.,Cell 31355-365 (1982)); the SV40 early promoter (Benoist, C., et al.,Nature (London) 290:304-310 (1981)); and the yeast gal4 gene promoter(Johnston, S. A., et al., Proc. Natl. Acad. Sci. (USA) 79:6971-6975(1982); Silver, P. A., et al., Proc. Natl. Acad. Sci. (USA) 81:5951-5955(1984)). All of the above listed references are incorporated byreference herein.

Strong promoters are preferred. Examples of such preferred promoters arethose which recognize the T3, SP6 and T7 polymerases, the P_(L) promoterof bacteriophage λ, the recA promoter and the promoter of the mousemetallothionein I gene. A most preferred promoter for eukaryoticexpression of RPTP is an SV40 promoter such as that drivingtranscription in the pLSV vector (Livneh, E., et al., (1986) J. Biol.Chem. 261, 12490-12497). The sequences of such polymerase recognitionsites are disclosed by Watson, J. D. et al. (In: Molecular Biology ofthe Gene, Fourth Edition, Benjamin/Cummings Publishing Co., Inc., MenloPark, Calif., (1987)).

Having now generally described the invention, the same will be morereadily understood through reference to the following example which isprovided by way of illustration, and is not intended to be limiting ofthe present invention, unless specified.

6. EXAMPLE Isolation and Analysis of Murine RPTPα cDNA Clones

6.1. Library Screening

A mouse BALB/C brain cDNA library in λgt11 (obtained from Dr. Y. Citri)was screened at relaxed stringency (6×SSC, 5×Denhardts, 0.1% SDS, 50 mMTris pH 7.5, 1 mM EDTA, 0.1 mg/ml salmon sperm DNA, hybridizationtemperature 50° C.) using as a probe a 2400 bp BglII-AccI fragmentrepresenting the intracellular and trans-membrane domains of the humanT200 glycoprotein (Ralph, S. J. et al., (1987) EMBO J. 6, 1251-1257),which had been ³²P-labeled using the random-priming method. Washing wasperformed at 50° C. in 6×SSC, 0.1% SDS. Out of 10⁶ clones, 51 positiveswere picked, selected and characterized by restriction enzyme mapping.EcoRI fragments of 0.95, 1.6 and 0.3 Kb isolated from the phage clonecontaining the longest insert (λ-109) were subcloned into the BluescriptKS plus and minus vectors. A series of nested deletions were generatedby taking use of restriction sites common to the cloned cDNA fragmentsand the polylinker region of the plasmid vector. The individualrestriction sites used are indicated in FIG. 1 b. Single stranded DNAwas prepared from these constructs, and used as a template for sequenceanalysis using the dideoxynucleotide chain termination method(Sequenase, United States Biochemical). All regions were sequenced onboth strands. The relative order and orientation of the EcoRI fragmentsin the recombinant phage was determined by restriction mapping. Toascertain that the different EcoRI fragments did not correspond tounrelated cDNA fragments ligated together during the process of libraryconstruction, restriction mapping was also performed on a different andindependent isolate, λ-113.

6.2. Results

Brain tissue already has proven to be a rich source of many types oftyrosine kinases, and recent biochemical evidence has also indicated theexistence of multiple forms of PTPase activity (Jones, S. W. et al.,(1989) J. Biol. Chem. 264, 7747-7753). In order to search for newreceptor-type PTPase, the present inventors screened at low stringency amouse brain cDNA library, using as a hybridization probe theintracellular domain of human CD45 containing two tandem PTPase domains(Tonks, N. K. et al., supra; Charbonneau, H. et al., supra; Ralph, S. J.et al., supra). Positive clones were classified by cross-hybridizationand restriction mapping into several categories, and the longest phageinsert (λ-109) corresponding to the most abundantly represented classwas chosen for subcloning and further analysis.

The result of the nucleotide sequence analysis is shown in FIG. 1, whichpresents the nucleotide sequence (SEQ ID NO:4) and the amino acidsequence (SEQ ID NO:3) of murine RPTPα. Conceptual translation of thecDNA sequence reveals the existence of a major open reading frame of 794amino acids, assuming that translation icnitiates at nucleotide 259 (anin-frame stop codon is present 60 nucleotides upstream). The putativeinitiation methionine codon is embedded in a relatively standardenvironment for initiation of translation (Kozak, M., (1987) Nucl. Ac.Res. 15, 8125-8148), and is followed by a characteristic hydrophobicstretch of amino acids which probably function as a signal peptide.According to the “−3, −1” rule (von Heijne, G. (1986) Nucl. Ac. Res. 14,4683-4690), residues 20 and 25 are both likely candidates to constitutethe N-terminus of the mature protein. A second hydrophobic stretch isfound between amino acids 143 and 166, and is followed by a series ofhighly charged residues, consistent with the stop-transfer signals foundto be associated with many membrane-spanning domains. The predictedintracellular domain of the protein consists of two tandem repeatshaving 44% sequence identity between each other (residues 259-486, and552-776). Each of these repeats display significant sequence identitywith the intracellular catalytic domains of the previously describedtransmembrane PTPase CD45 (Ralph, S. J. et al., supra) and LAR (Streuli,M. et al., (1988), supra) (45% and 53% amino acid sequence identity,respectively).

In contrast, the EMBL and GENBANK databases contain no significanthomology to known sequences of the putative extracellular domain of theencoded protein. Features of the extracellular domain include a uniquelyhigh content of serine and threonine residues (>32%), the absence ofcysteine residues, and the presence of 8 potential N-linkedglycosylation sites.

It was concluded that the isolated cDNA encoded a new member of thetransmembrane PTPase family having a novel type of extracellular domain.In view of its receptor-like structure and the likelihood thatadditional members of this family can be found based on the presentexperimental evidence, the name muRPTPα (murine receptor proteintyrosine phosphatase-α) was chosen to designate this protein.

7. EXAMPLE Chromosomal Localization of the Mouse RPTPα Gene

STS/A, 020/A, CXS and OXA recombinant inbred (RI) mice, and CXB RIstrains N, O, P, Q, and R were a gift from Dr. Jo Hilgers (TheNetherlands Cancer Institute). All other inbred mice were purchased fromthe Jackson Laboratory (Bar Harbor, Me.). Backcross (BC) animals werebred at New York University with inbred progenitors obtained from theJackson Laboratory. The female parent is named first in all crosses andF1 designations.

Spleen genomic DNA from the AKXD, AKXL, BXD, BXH and G, H, I SWXL RIstrains, and from CXB, RI strains D, E, G, H, I, J, and K was purchasedfrom the DNA Resource at the Jackson Laboratory. For all other mice,genomic DNA was prepared from crude liver nuclei by a standard sequenceof protease digestion, phenol and chloroform extraction, and ethanolprecipitation. Mouse genomic DNAs were subjected to Southern blottinganalysis by slight modifications of standard procedures, exactly asdescribed previously (Silver, J. (1985) J. Hered. 76, 436-440). A 1.8 kbEcoRI fragment corresponding to the intracellular phosphatase domains ofRPTPα, and a 0.7 kb SacII-EcoRI fragment corresponding to itsextracellular and transmembrane domains, were cloned into the BluescriptKS vector, yielding plasmids p109 and p923, respectively.

DNA restriction fragment length variants associated with the Il-1a locus(interleukin-1 alpha) were detected by Southern blotting as describedpreviously (D'Eustachio, P. et al., (1987) Immunogenetics 26, 339-343).The significance of deviations from 1:1 segregation for pairs of markerswas calculated by the Bayesian method of Silver and Buckler (Silver, J.et al., (1986) Proc. Natl. Acad. Sci. USA 83, 1423-1427); Blank, R. D.et al., (1988) Genetics 120, 1073-1083). Map distances were estimatedfrom recombination fractions measure in RI strain sets according to B.A. Taylor (in: Morse, H. C. III, ed., Origins of Inbred Mice, AcademicPress, New York, 1978, pp. 423-438), and their associated 95% binomialconfidence limits were calculated according to Silver (1985, supra).Probabilities of alternative orders of trios of markers were calculatedaccording to D. Bishop ((1985) Genet. Epidemiol. 2, 349-361, equation1). Computations were carried out on a VAX6000-410 computer.

Southern blotting analyses of genomic DNA from inbred strains of micerevealed two useful restriction length variants, one visualized with aprobe corresponding to the intracellular domain of murine RPTPα (p109)and one visualized with an extracellular and transmembrane domains probe(p923). Together, these variants allowed definition of three allelicforms of muRPTPα among the 10 inbred strains of mice surveyed (Table I).TABLE I Restriction Fragment Length Variants Detected by muRPTPα ProbesProbe Allele p109 p923 Mouse Strains a 9.4 5.9 + 4.2 BALB/cJ b 6.5 4.2 +1.8 C57BL/6J, C57L/J, DBA/2J c 6.5 5.9 + 4.2 C3H/HeJ, 020/A, AKR/J,SWR/J, SJL/J, STS/ALiver genomic DNA digested with TaqI restriction endonuclease wasanalyzed by Southern blotting. Fragment sizes in kilobases are shown.

Inheritance of these alleles in RI mice was scored. Comparison of thestrain distribution patterns observed for murine RPTPα (Table II) withthose previously observed for other markers of known chromosomallocation in these mice indicated close linkage between the muRPTPα andIl-1a (Interleukin-1) loci on chromosome 2 (3 RI strains among 89examined). This degree of concordance has a probability of less than0.00001 of occurring as a chance event were the loci unlinked. Theobserved fraction of recombinant strains indicates a map distance of 0.9cM between the loci (95% confidence limits 0.2-0.6 cM). TABLE IIInheritance of muRPTPα and Il-1a DNA sequence variants in RI strains ofmice AKXD strain:               1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 1 2 36 7 8 9 0 1 2 3 4 5 6 8 0 1 2 3 4 5 6 7 8 Il-1a D D D A D A A D D A D AD A D A D A D A D A A A R-PTP-α D D D A D A A D A A D A D A D A D A D AD A A A AKXL strain:                         SWXL strain:           1 11 1 1 1 2 2 2 2 2 3 3      1 1 1 1 1 5 6 7 8 9 2 3 4 6 7 9 1 4 5 8 9 78  4 7 2 4 5 6 7 Il-1a L L L A L A L L L A A L A L A L A L  S L S L L SL R-PTP-α L L L A L A L L L A A L A L A L A L  S L S L L S LCXB strain:              CXS strain:                                           1 1 1 1 1 D E G H I J K N O PQ R  1 2 3 4 5 6 7 8 9 0 1 2 3 4 Il-1a C B B C B B B C C C C B  T T T CC T T T C T C C T C R-PTP-α C B B C B B B C B C C B  T T T C C T C T C TC C T C BXH STRAIN:              BXJ strain:               1 1 1 1 1 2 34 6 7 8 9 0 1 2 4 9  1 2 Il-1a B B H H B H B H B H H B  B B R-PTP-α B BH H B H B H B H H B  B BRI strains were typed for alleles of muRPTPα and Il-1a by Southernblotting of TaqI-digested DNA (see Table I and D'Eustachio, P. et al.,Immunogenetics 26, 339-343 (1987)). Il-1a alleles for AKXD, CXB strainsD-K, and BXH mice were disclosed in D'Eustachio et al., supra). All RIstrains are homozygous for one of the progenitor strain alleles at eachlocus; the allele is# indicated by an uppercase letter corresponding to the parent strain asfollows: A, AKR/J; B, C57BL/6J; C, BALB/c; D, DBA/2J; H, C3H/HeJ; J,SJL/J; L, C57L/J; S, SWR/J; T, STS/A.

Following the inheritance of muRPTPα, Il-1a and a (nonagouti) amongprogeny of reciprocal backcross between the C57BL/6J and SWR/J strainsconfirmed the linkage of muRPTPα and Il-1a, and suggested an order forthe two genes (Table III). Of 150 progeny, 14 were recombinant betweenmuRPTPα and a, and one was recombinant between muRPTPα and Il-1a. If thelocus order were: centromere—Il-1α—muRPTPα—a, these results wouldrequire the occurrence of no double crossovers; alternative ordersrequire one or 14 such events, and, evaluated according to the method ofBishop (supra), are at least 9.5-fold less likely. The distance betweenIl-1a and muRPTPα, 0.6 cM (95% confidence limits: 0.1-2.4 cM), agreeswithin sampling fluctuation with the distance estimated from the RIstrain data. Comparison of these results with results recently obtainedfor Bmp-2a (Bone morphogenic protein 2a, Dickinson, M. E. et al., (1990)Genomics 6, 505-520) suggests that the two genes may be closely, linked,although there is no obvious structural, homology between them. TABLEIII Linkage Among Markers of Chromos me 2 in Backcross BC Progeny A.ALLELE COMBINATIONS FROM F₁ PARENT AND THE ACTUAL NUMBERS OFC57BL/6J-DERIVED (b) AND SWR/J-DERIVED (s) ALLELES FOUND LOCUS POSSIBLEALLELE COMBINATION Σb Σs Il-1a b s b s b s b s 76 74 R-PTP-α b s b s{dot over (s)} {dot over (b)} {dot over (s)} {dot over (b)} 77 73 a b s{dot over (s)} {dot over (b)} s b {dot over (b)} {dot over (s)} 69 81 B.NUMBERS OF PROGENY FROM EACH BACKCROSS THAT INHERITED EACH POSSIBLEALLELE COMBINATION. BACKCROSS NUMBER OF PROGENY F₁ × B 44 43 9 1 0 1 0 0B × F₁ 21 27 2 2 0 0 0 0 135 14 1 0150 progeny from BC between (C57BL/6J × SWR/J)F₁ (F1) and C57BL/6J (B)mice were typed visually for inheritance of the nonagouti (a) markerand, by Southern blotting, for alleles of the muRPTPα and Il-1a loci.

8. EXAMPLE Expression of Murine RPTPα RNA

8.1. Northern Analysis

Poly A⁺ RNA was prepared from adult mouse tissues and cell lines byoligo(dT) selection as described (Vennström, B. et al., (1982) Cell 28,135-143), fractionated (5 μg per lane) on a formaldehyde-containing geland transferred to nitrocellulose (Hybond C, Amersham) using standardprocedures. A ³²P-labelled probe was prepared by primer extension on asingle-stranded template consisting of the entire λ-109 cDNA cloned intothe EcoRI site of the Bluescript vector in the antisense orientation,using the Klenow fragment of DNA polymerase for elongation from anannealed T7 primer, in the presence of ³²P-dATP. Hybridization wasperformed at 42° C. in 50% formamide, 5×SSC, 25 mM KPO₄, 5× Denhardt's,10 μg/ml salmon sperm DNA, and 10% sulfate. Washing was done at 48° C.in 0.1×SSC, 0.1% SDS. Higher stringency washes (58° C.) of the filterdid not noticeably affect the hybridization pattern.

8.2. Expression of the Murine RPTPα Protein.

The entire cDNA insert from phage λ-109 was released as one fragmentfrom the phage using partial EcoRI digestion, and cloned into theBluescript KS vector. A cDNA fragment lacking most of the untranslatedleader sequence (starting from the Sac II site at position 226; see FIG.1 b) was subcloned into the SV40 promoter driven PLSV-vector (Livneh,E., et al., (1986) J. Biol. Chem. 261, 12490-12497), and the resultingplasmid DNA (pLSV-PTP-α) was transfected into COS cells using theDEAE-dextran method (Lopata, M. A. et al., (1984) Nucl. Ac. Res. 12,5707-5717). The expression vector pLSVΔC encoding the N-terminallytruncated muRPTPα protein was used as a control in theimmunoprecipitation experiment.

8.3. Results

Poly A⁺ RNA from various mouse tissues was prepared to study theexpression of the muRPTPα gene. Northern analysis (FIG. 2) revealed awide pattern of expression. A 3.0 kB mRNA was present in all tissuesexamined, except spleen, with brain and kidney showing the highestlevels of expression. An mRNA of similar size could also be observed inthe NIH-3T3 mouse fibroblast line, 2.2, and the prepro-B lymphoid cellline, BAF (FIG. 2). Shorter exposure of the Northern blot clearly showedthat in addition a second mRNA species of very similar size. (3.2 kb) ispresent in several tissues (e.g. brain) in lower amounts. The data alsosuggest that, although a poly A tail and a polyadenylation signal at the3′ end of the cDNA sequence were not observed, the isolated cDNA clone(2872 nucleotides) closely matches the full length of the mRNA.

9. EXAMPLE Transient Expression of the Murine RPTPα Protein

9.1. Antibody Preparation and Immunoprecipitation

Rabbits were injected with a synthetic peptide corresponding to thepredicted C-terminus of the muRPTPα protein (residues 777-794) coupledto BSA using EDCI (1-ethyl-3-(dimethylaminopropyl)carbodiimide) as acoupling reagent. Antigen was injected intradermally and subcutaneouslyin an emulsion of 1 mg peptide and complete Freund's adjuvant. Threebooster injections were given at 2-3 week intervals with 0.5 mg peptideand incomplete adjuvant. An antiserum obtained using this method wasdesignated “2A.” Metabolic [³⁵S]-methionine labelling, cell extractpreparation (60 hours after transfection) and indirectimmunoprecipitation using protein-A-Sepharose were performed usingstandard procedures (Yarden, Y. et al., (1987) EMBO J. 6, 3341-3351).

9.2. Results

In order to determine the size of the mature protein, we cloned themuRPTPα cDNA with the exception of most of the untranslated leader intothe pLSV vector (Livneh, E., et al., (1986) J. Biol. Chem. 261,12490-12497) under the control of the SV40 promoter, yielding theexpression vector pLSV-PTP-α. The vector was transfected into COS cells,and 60 hours later [³⁵S]-methionine labelled total cell extracts wereprepared for immunoprecipitation, using antiserum 2A.

As seen in FIG. 3, the antiserum recognized several bands, one of which,a diffuse band of 130 kDa (arrow), was only present inimmunoprecipitates from transfected cells (lane 5), but not frommock-transfected cells (lane 3) (transfected with pLSV without themuRPTPα cDNA). Precipitation could be competed out by the peptide usedfor immunization (lane 6).

The difference between the predicted (88 kDa) and observed (130 kDa)molecular weights for the muRPTPα protein is ascribed to its extensiveglycosylation.

As an additional control for the specificity of the antiserum, we alsotransfected COS cells with a N-truncated version of the muRPTPα cDNA(starting at amino acid 214, and thus lacking the transmembrane andextracellular domains) in the same vector. A new and abundant proteinwith an apparent molecular weight of 55 kDa appeared inimmunoprecipitates from cells transfected with this vector, which wasagain competed out by the antigenic peptide (lanes 7 and 8). The higherabundance of the truncated protein as compared to the mature muRPTPαprotein was a consistent observation over several independenttransfection experiments.

9.3. General Discussion for Sections 6-9

The Examples presented above describe the identification of a novelreceptor-like PTPase, RPTPα, having a broad pattern of expression. RPTPsare therefore expected to have widespread functions beyond theregulation of lymphoid cell activity, as was previously thought based onstudy of CD45.

Studies using monoclonal antibodies directed, against the extracellulardomain of CD45 proteins showed that cross-linking of RPTPs can haveprofound effects on various cellular activities, although a directeffect on PTPase enzymatic activity remains to be shown. However, sinceligand-induced receptor clustering is a central event in transmembranesignalling by receptor tyrosine kinases (Ullrich, A. et al., supra), itis proposed by the inventors that putative extracellular ligands forRPTPs have the capacity to regulate the activity of RPTPs in vivo.

In a manner analogous to that proposed for receptor tyrosine kinases(PTKs), RPTPs are proposed to have arisen through several gene fusionevents between an ancestral PTPase domain, and domains capable ofbinding extracellular ligands (Ullrich, A. et al., Hanks, S. K. et al.,supra.).

The variety of extracellular domains potentially joined to PTPasedomains to form receptor-like proteins are expected to reflect the rangeof possible ligands able to act by similar mechanisms. The availabilityof cloned RPTPs, such as those disclosed herein, will be valuable indetermining their substrate specificity and in understanding theirfunction and manipulating their activity.

RPTPs might have a broad specificity directed towards major tyrosinekinase substrates, with their different extracellular domains mainlyallowing for different regulatory mechanisms responsive to differentsignals in the extracellular environment. Based on this view, they areexpected to modulate the responsiveness of a cell to those polypeptidegrowth factors which act through receptor protein tyrosine kinases. Aswith PTK's, ligand binding would lead to an activation of enzymaticactivity. Viewed in this light, RPTPα and molecules like it, would benegative growth regulators and can be considered potential recessiveoncogenes.

For instance, deletion of portions of murine chromosome 2, to whichRPTPα maps, appears to be an early event in the development ofradiation-induced myeloid leukemia in SJL/J mice (Tracktenbrot, L. etal., (1988) Leukemia 2, 545-550), consistent with the recessive oncogenenotion. Furthermore, rearrangements involving human chromosome 20 (towhich the human RPTPα gene maps) have been linked to human lymphoidleukemia (Mitelman, F. (ed.) Catalog of Chromosome Aberrations in HumanCancer, A. Liss, New York).

Alternatively, RPTPα may act in a manner analogous to that proposed forthe interaction between CD45 and c-lck (Oostergaard, H. L. et al.,(1989) Proc. Natl. Acad. Sci. USA 86, 8959-8963; Mustelin, T. et al.,(1989) Proc. Natl. Acad. Sci. USA 86, 6302-6306). According to thisview, RPTPα would dephosphorylate negative regulatory sites inmembrane-associated PTKs which are not receptors, and which are morewidely expressed than lck (such as, for example, the tyr⁵²⁷ site inpp60^(c-src)). Acting in this manner, RPTPα would be implicated inpositive growth control and differentiation.

Although the inventors do not intend to be bound by any particulartheory, the high interspecies conservation of the catalytic domains ofthe various RPTPs indicate an important role for these receptors in cellgrowth control.

10. EXAMPLE Isolation and Characterization of Human RPTP cDNA (See,also, Kaplan, R. et al., Proc. Natl. Acad. Sci. USA 87:7000-7004 (1990))

10.1. Materials

Restriction endonucleases and modifying enzymes were purchases fromBoehringer-Mannheim or New England Biolabs. Taq DNA polymerase was fromPerkin-Elmer/Cetus. The λgt11 forward and reverse primers (24-mers) usedin the polymerase chain reactions as well as all sequencing primers,were synthesized on an automated DNA synthesizer (Applied Biosystems,model 380A) using either methoxy or β-cyanoethyl phosphoramidites(House, C., et al., J. Biol. Chem., 262:772-777 (1987)). The λgt11 humanbrainstem cDNA library was obtained form the American Type CultureCollection (no. 37432). The LCA (CD45) clone used as a probe forscreening the library was received from E. H. Fischer (University ofWashington, Seattle). All sequencing reactions were performed using theSequenase kit (United States Biochemical).

10.2. Methods

Approximately 300,000 plaques from a λgt11 cDNA library of 1-day-oldhuman infant brainstem were screened on duplicate nitrocellulose filtersunder conditions of reduced stringency with a nick-translated LCA probethat spanned both conserved phosphatase domains (Charbonneau, H. et al.,1989, supra).

Hybridization was carried out at 55° C. overnight in a solution of5×SSPE (SSPE is 10 mM NaH₂PO₄, pH 7.4/0.18 M NaCl/1 mM EDTA) containing0.25% nonfat dry milk, 0.1% SDS, and ³²P-labeled LCA probe at 10⁶cpm/ml. The filters were washed three times for 20 min at 55° C. in2×SSPE/0.2% SDS and then processed for autoradiography. This screenyielded 79 duplicate positives; 12 of these, showing varying degrees ofhybridization to the LCA probe, were plaque-purified by repetitionscreening with the same probe. The polymerase chain reaction (Saiki, R.K., et al., Science, 230:1350-1354 (1985)) was then used to determinethe sizes of the cDNA inserts. The DNA templates consisted of portionsof the eluates from each pure plaque, heated at 75° C. for 15 min. torelease the DNA. The templates were primed with the λgt11 forward andreverse primers. The reaction mixtures (0.1 ml) were prepared asdescribed (Dionne, C. A. et al., Biotechniques 8:190-194 (1990)).Amplification was achieved by performing 30 cycles, each including 1.5min of denaturation at 94° C., 2 min of annealing at 65° C., and 4 minof extension at 72° C., in an automated Perkin-Elmer/Cetus DNA thermalcycler. A portion of each sample (15 μl) was analyzed by electrophoresisthrough, a 1% agarose gel containing ethidium bromide at 1 μg/ml(Sambrook et al., supra). DNA was prepared from the 4 largest clones byusing LambdaSorb (Promega) and then digested with EcoRI. The fragmentswere subcloned separately into the EcoRI site of M13mp18 for sequencing.Nucleotide sequences were determined by the dideoxynucleotidechain-termination method (Sanger, F., et al., Proc. Natl. Acad. Sci.USA, 74:5463-5467 (1977)) using modified T7 polymerase (Tabor, S. etal., Proc. Natl. Acad. Sci. USA 84:4767-4771 (1987)).

All computer analyses of sequence data were performed on a Micro VAX IIusing programs written by IntelliGenetics. DNA sequences were analyzedand assembled using the GEL program. Hydrophobic analyses of proteinswere based on the algorithm of Kyte and Doolittle (Kyte, J. et al., J.Mol. Biol. 157:105-132 (1982)), as implemented in the PEP program.Protein sequence alignments were done using the GENALIGN program (Sobel,E. et al., Nucleic Acids Res. 14:363-374 (1985); Karlin, S. et al., Mol.Biol. Evol. 1:357-370 (1984); Needleman, S. B. et al., J. Mol. Biol.48:443-453 (1970)). Initial alignments were done using theJimenez-Montano protein alphabet (Jimenez-Montano, M. et al., Proc. 7thInt'l. Biophysics Congress, 1981, Mexico City).

10.3. Results

In an effort to identify new members of the PTPase family, 300,000plaques from a human infant brainstem cDNA library in λgt11 werescreened under nonstringent conditions using a nick-translated LCA probethat spanned both conserved phosphatase domains. Four of the initial 79duplicate positives were sequenced in the entirety. Two clones, 31-4 and27-1, contained overlapping portions of the entire coding region of ahuman RPTP (huRPTP) that was designated RPTPα (FIGS. 4 and 8). Thecombined lengths of clones 31-4 and 27-1 equaled 3615 bp (FIG. 4A),encoding a protein of 802 amino acids (FIG. 4D) and containing anadditional 695 bp and 510 bp, respectively, of 5′ and 3′ untranslatedregion. Two of the four clones contained portions of genes coding fortwo additional RPTPs which have been designated B and γ (FIG. 5). LikeRPTPα, these two proteins contain typical hydrophobic transmembraneregions and distinct extracellular domains, indicating that they alsorepresent separate RPTPs.

Thus, the nucleotide sequence of human RPTPα (SEQ ID NO:2)is shown inFIG. 8. The deduced amino acid sequence of the human RPTPα protein (SEQID NO:1) is shown in FIGS. 4D and 8.

The murine homologue of human RPTPα is described in Sections 6-9, above.A comparison of the mouse and human protein sequences (FIG. 4D)indicates that, with the exception of the extracellular domain, wheresome variability exists, only 5 residues are found to differ between thetwo proteins.

An examination of the structure of human RPTPα reveals the followingfeatures: a relatively short extracellular domain consisting of 150residues that includes a hydrophobic signal peptide containing the onlycysteine in this region. There are eight potential N-glycosylationsites, as well as a number of potential O-glycosylation sites (sincethis domain is rich in serine and threonine). The extracellular domainsof RPTPα and the LCA and LAR molecules described by others appear to bestructurally unrelated. Human RPTPα has a hydrophobic transmembraneregion anchored on both sides by charged residues. This is followed bythe two tandemly repeated conserved phosphatase domains of about 235residues each, which are separated by 57 amino acids, typical of RPTPssuch as LCA, LAR and the two Drosophila PTPases, DLAR and DPTP.

FIGS. 5A and 5B show the alignments of the amino acids within the firstand second conserved phosphatase domains, respectively, of LCA and RPTPsα, β, and γ. It is readily apparent that among the four RPTPs, β and γshare the greatest sequence similarity. It was reported (Hunter, T. etal. supra) that among the sequences of the conserved phosphatase domainsof PTPase 1B, LCA, LAR, DLAR and DPTP there are 29 invariant residues.While many of these residues are also present in both phosphatasedomains of RPTPα, β, and γ, it is interesting that the second conservedphosphatase domains of both β and γ lack a number of these amino acids,including the two cysteines at positions 104 and 201 in phosphatasedomain 2 of LCA (see FIG. 5B).

10.4. Discussion

The sequences of the conserved phosphatase domains of the three humanRPTPs identified here (α, β, and γ) have been compared with one anotheras well as with those of LCA, LAR, and two soluble PTPases, placentalphosphatase 1B and T-cell PTPase (Table IV). The two soluble enzymeshave a sequence identity of 70%; however, when each is compared with theRPTPs (Phosphatase domains PD1 or PD2), this number drops to 29-42%. Inall cases, the soluble PTPases showed a greater identity with PD1 thanwith PD2 of the RPTPs. RPTPα appears to be most related to LAR, sincetheir PD1 sequences are 56% identical and their PD2 sequences are 52%identical. The conserved domains of RPTPβ and RPTPγ are most related toeach other, even more so than are the two soluble PTPases, β and γ being75% identical in both PD1 and PD2. It is interesting that, in general,the sequence relationship between PD1 and PD2 within any RPTP appears tobe no closer than that seen between different members of the family,i.e., the identities between PD1 and PD2 range from a high of 47% forLAR to a low of 29% for RPTP γ.

While the cytoplasmic domains of RPTPα, β, and γ are highly conserved,the extracellular domains of these receptors are unrelated to oneanother as well as to those of LAR and LCA. This suggests that each ofthese receptors has its own distinct ligand. It is likely that thebinding of such ligands to the RPTPs plays a crucial role, together withgrowth factor receptors exhibiting PTKase activity, in the regulation ofthe level of tyrosine phosphorylation of targets proteins involved insignal transduction. The diversity of the RPTPs described herein revealsthe existence of a multigene family. Greater understanding ofstructure-function relationships among these membrane receptors willprovide important insights into the mechanisms involved in cell growth,differentiation, and oncogenesis. TABLE IV Identities Between ConservedPhosphatase Domains (Percent) PTPase T-cell LCA LAR RPTPaseα RPTPase-βRPTPase-γ 1B PTPase PD1 PD1 PD1 PD2 PD1 PD2 PD1 PD2 PD1 PD2 PTPase 1B100 . . . . . . . . . . . . . . . . . . . . . . T-cell PTPase 70 100 . .. . . . . . . . . . . . . . . . . . LCA PD1 37 36 100 . . . . . . . . .. . . . . . . . . LCA PD2 30 26 31 100 . . . . . . . . . . . . . . . .LAR PD1 39 42 50 28 100 . . . . . . . . . . . . . . LAR PD2 29 33 42 3445 100 . . . . . . . . . . . . RPTPα PD1 36 38 50 32 56 45 100 . . . . .. . . . . RPTPα PD2 33 34 40 32 41 52 43 100 . . . . . . . . RPTPβ PD135 39 41 31 33 41 47 33 100 . . . . . . RPTPβ PD2 29 30 31 30 31 34 3137 30 100 . . . . RPTPγ PD1 35 34 32 29 39 36 34 32 75 27 100 . . RPTPγPD2 29 29 30 28 32 36 31 34 33 75 29 100Alignments of the conserved phosphatase domains were carried out asdescribed above. The regions compared are designated in FIG. 4C and FIG.5. PD = phosphatase domain.

11. EXAMPLE Expression of Human RPTPα by Northern Blot Analysis

Samples containing either 20 μg of total RNA or 2 μg of poly(A)⁺ RNAwere resolved in a formaldehyde/agarose gel and transferred tonitrocellulose. RPTPα and β-actin probes were labeled by random priming(Sambrook et al., supra). Hybridizations and washes were carried out at65° C. as described (Church, G., et al., Proc. Natl. Acad. Sci. USA,81:1991-1995 (1984)). Blots hybridized with the RPTPα probe were exposedto XAR-2-x-ray film (Kodak) with an intensifying screen for 72 hr at−80° C. Results were obtained from the actin-probe blots after 15 hrunder the same conditions.

RPTPα expression was examined in various cell lines and tissues (FIG.6). The results indicate the presence of two major RNA transcripts ofapproximately 4.3 and 6.3 kb, respectively. The larger of the twospecies appears to be more prevalent in fetal tissues and inparticularly prominent in the poly(A)⁺ fetal liver sample, where thereis also the highest relative amount of the 4.3-kb transcript. It ispossible that the different expression of the two transcripts isdevelopmentally regulated and/or a result of alternative splicingmechanisms, a feature seen with LCA (Ralph, S. J. supra). The adultbrain shows relatively less expression of RPTPα. The results suggestthat RPTPα is expressed to some degree throughout many tissues. MurineRPTPα was also shown to be expressed in many tissues and cell lines andmost abundantly in brain and kidney (Sap, J., et al., Proc. Natl. Acad.Sci. USA, 87:6112-6116, (1990); see also Sections 8 and 9, above).

12. EXAMPLE Chromosome Localization of the Human RPTPα Gene

Isolation, propagation, and characterization of parental and somaticcell hybrids using in this study have been described (Durst, M. et al.,Proc Natl. Acad. Sci. USA 84:1070-1074 (1987); Ku, D-H. et al., SomaticCell Mol. Genet. 15:297-307 (1989); Juan, C-C. et al., Proc. Natl. Acad.Sci. USA 85:8910-8913 (1988)). Presence of specific human chromosomes orregions of chromosomes has been confirmed by DNA hybridization usingprobes for genes assigned to specific chromosome regions. Hybrid DNAswere digested with an excess of restriction endonuclease HindIII orEcoRI, sized by electrophoresis in 0.8% agarose gels, transferred tonylon filters, and hybridized as described (Durst et al., supra). TheRPTPα probe consisted of the 3′-most 0.8 kilobases (kb) of clone 31-4(see FIG. 4B).

DNAs from 17 rodent-human somatic cell hybrids carrying overlappingsubsets of human chromosome regions representing the entire human genomewere tested for presence of the human RPTPα locus by Southern blotanalysis. The results (FIG. 7) show that presence of the human RPTPαlocus in hybrid cells correlates only with presence of a partial humanchromosome 20. The data also allow a regional localization for the RPTPαlocus, since hybrids PB5-1 and AB3 are each missing a part of the longarm of chromosome 20 and yet retain the RPTPα locus. Thus, the humanRPTPα gene maps to 20pter-20q12.

Murine homologues of all human genes which have been mapped to humanchromosome 20 map to mouse chromosome 2 (Lalley, P. A. et al.,Cytogenet. Cell Genet. 51:503-532 (1989)). This appears to be true forRPTPα as well (see Section 7,above). The long arm of human chromosome 20is involved in translocation and deletions in myeloid disorders andneoplasms (Trent, J. M., et al., Cytogenet. Cell Genet., 51:533-562,(1989)). The human RPTPα locus may be specifically involved in deletionon 20q; in this case, it would strengthen the possibility of it being atumor-suppressor gene or anti-oncogene. Similarly in mice, in the SJL/Jstrain, deletion of chromosome 2 appears to be involved in thedevelopment of radiation-induced myeloid leukemia (Trakhtenbrot, L., etal., Leukemia, 2:545-550, (1988)).

The references cited above are all incorporated by reference herein,whether specifically incorporated or not.

Having now fully described this invention, it will be appreciated bythose skilled in the art that the same can be performed within a widerange of equivalent parameters, concentrations, and conditions withoutdeparting from the spirit and scope of the invention and without undueexperimentation.

While this invention has been described in connection with specificembodiments thereof, it will be understood that it is capable of furthermodifications. This application is intended to cover any variations,uses, or adaptations of the inventions following, in general, theprinciples of the invention and including such departures from thepresent disclosure as come within known or customary practice within theart to which the invention pertains and as may be applied to theessential features hereinbefore set forth as follows in the scope of theappended claims.

1-10. (Canceled)
 11. A method for detecting in a subject the presence ofa nucleic acid molecule comprising a nucleotide sequence that (i)encodes a polypeptide having the amino acid sequence SEQ ID No: 1 or SEQID No: 3; (ii) is the complement of the nucleotide sequence of (i); or(iii) hybridizes under highly stringent conditions to the nucleic acidmolecule of (i) or (ii), comprising: (a) contacting a cell or an extractthereof from said subject with a nucleic acid probe comprising at leasta portion of the nucleic acid molecule of (i), (ii), or (iii) underhighly stringent conditions; (b) measuring the hybridization of saidprobe to the nucleic acid molecules of said cell or an extract thereof,thereby detecting the presence of said nucleic acid molecule.
 12. Themethod of claim 11, additionally comprising before step (a): selectivelyamplifying said nucleic acid molecule of (i), (ii), or (iii).
 13. Themethod of claim 11 or 12, wherein highly stringent conditions comprisehybridizing at 42° C. in 50% formamide, 5×SSC, 25 mM KPO₄, 5×Denhardt's, 10 μg/ml salmon sperm DNA and 10% sulfate followed bywashing at 58° C. in 0.1×SSC and 0.1% SDS.